/data/tool/gcphrap aa.fasta.screen -ace -view -exp /data/ultra_disk/people/tomato/t1/C03HBa0049i23/workdir/all.assembly 
gcphrap version 0.990319

Run date:time  081127:113654
Query file(s):  aa.fasta.screen
Presumed sequence type: DNA

Pairwise comparison algorithm: banded Smith-Waterman

Score matrix (set by value of penalty: -2)
    A   C   G   T   N   X
A   1  -2  -2  -2   0  -3
C  -2   1  -2  -2   0  -3
G  -2  -2   1  -2   0  -3
T  -2  -2  -2   1   0  -3
N   0   0   0   0   0   0
X  -3  -3  -3  -3   0  -3

Gap penalties: gap_init: -4, gap_ext: -3, ins_gap_ext: -3, del_gap_ext: -3, 
Using complexity-adjusted scores. Assumed background frequencies:
 A: 0.250  C: 0.250  G: 0.250  T: 0.250  N: 0.000  X: 0.000  

minmatch: 14, maxmatch: 30, max_group_size: 20, minscore: 30, bandwidth: 14, indexwordsize: 10
vector_bound: 80
word_raw: 0
trim_penalty: -2, trim_score: 20, trim_qual: 13, maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8, confirm_trim: 1, confirm_penalty: -5, confirm_score: 30
node_seg: 8, node_space: 4
forcelevel: 0
max_subclone_size: 5000

Sequence file: aa.fasta.screen    966 entries
Residue counts:
  A    254650
  C    152492
  G    145739
  N     1148
  T    284425
  X    188459
Total  1026913

Read name analysis:
 # Reads      # templates
   1           966

 Suffix counts:
(no suffix) 966


Templates inferred from description field:     0
Templates inferred from name field:          966

Read-template multiplicity analysis:
 # Reads      # templates
   1           966

Chemistries inferred from description field:
    0  dye-primer
    0  old-dye-terminator
    0  big-dye-terminator
    0  other

Chemistries inferred from name:
  966  dye-primer
    0  old-dye-terminator
    0  big-dye-terminator
    0  other

Directions inferred from description field:
    0  fwd
    0  rev
    0  unknown (set to fwd)

Directions inferred from name:
    0  fwd
    0  rev
  966  unknown (set to fwd)

Quality file: aa.fasta.screen.qual

Input quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56  184187  17.9  184187  17.9    0.46
 51   40001   3.9  224188  21.8    0.78
 50   38709   3.8  262897  25.6    1.17
 48    3164   0.3  266061  25.9    1.22
 47    6437   0.6  272498  26.5    1.35
 46    9477   0.9  281975  27.5    1.58
 45    7734   0.8  289709  28.2    1.83
 44   29665   2.9  319374  31.1    3.01
 43   18847   1.8  338221  32.9    3.95
 42   56955   5.5  395176  38.5    7.55
 41    6211   0.6  401387  39.1    8.04
 40   35301   3.4  436688  42.5   11.57
 39    1779   0.2  438467  42.7   11.80
 38    3251   0.3  441718  43.0   12.31
 37   19563   1.9  461281  44.9   16.21
 36    2008   0.2  463289  45.1   16.72
 35   17262   1.7  480551  46.8   22.18
 34    6414   0.6  486965  47.4   24.73
 33   10530   1.0  497495  48.4   30.01
 32    7899   0.8  505394  49.2   34.99
 31    4378   0.4  509772  49.6   38.47
 30    5371   0.5  515143  50.2   43.84
 29   17079   1.7  532222  51.8   65.34
 28    5653   0.6  537875  52.4   74.30
 27    7986   0.8  545861  53.2   90.24
 26    3528   0.3  549389  53.5   99.10
 25   10131   1.0  559520  54.5  131.13
 24    8250   0.8  567770  55.3  163.98
 23    7324   0.7  575094  56.0  200.68
 22    6249   0.6  581343  56.6  240.11
 21    8882   0.9  590225  57.5  310.67
 20    7795   0.8  598020  58.2  388.62
 19   12182   1.2  610202  59.4  541.98
 18    8938   0.9  619140  60.3  683.64
 17    9768   1.0  628908  61.2  878.53
 16   11678   1.1  640586  62.4  1171.87
 15   14525   1.4  655111  63.8  1631.19
 14   13412   1.3  668523  65.1  2165.13
 13   21504   2.1  690027  67.2  3242.89
 12   20973   2.0  711000  69.2  4566.19
 11   34559   3.4  745559  72.6  7311.31
 10   43333   4.2  788892  76.8  11644.61
  9   78306   7.6  867198  84.4  21502.75
  8   62964   6.1  930162  90.6  31481.87
  7   42456   4.1  972618  94.7  39952.96
  6   46625   4.5  1019243  99.3  51664.63
  4    6483   0.6  1025726  99.9  54245.56
  0    1164   0.1  1026890 100.0  55409.56
 -1      23   0.0  1026913 100.0  55432.56   (quality -1 = terminal quality 0)

Avg. full length: 1063.1, trimmed (qual > -1): 1063.0
Avg. quality: 30.0 per base

Exact duplicate reads:  None.

Probable unremoved sequencing vector (matches excluded from assembly, quality reduced to 0): 
aa010109f1   18-26   CTGCAGCCC
ab090109r1    8-69   TTTATTTTATTTATTATTATTGTATCCGCGGGGGCGGCCGCTCTAGTACTAGTGGATCCCCC
ab100109r1    9-47   CTCCCGCCGGTGGCGGCCGCTCTAGACTAGTGGACCCCC
ac030109r1    9-49   CCCCGCCGGTGGGCGGCCGCTCTAGAACTAGTGGATCCCCC
ac080109f1    9-32   TAACGAAATCCCTGCAGCCCCTTC
ac080109r1   19-49   GGCGGCCGCTCTAGAAACTAGTGGATCCCCC
ad090109f1   14-25   TTCCTGCAGCCC
ae030109r1    1-45   GTGTGATCCCCGCGGGGGGCGGCCGCTCTAGACTAGTGGACCCCC
ae110109f1    7-24   AACGAAATCCTGCAGCCC
ae120109f1   11-26   CGAAATCCTGCAGCCC
ag100109r1   11-47   CGGGTGGCGGCCGCTCTAGAACTAGTTGGATCCCCCT
ah040109f1    7-25   ATCGAATTTCCTGCAGCCC
bb050109f1    2-25   AAATTGAATCGGATTCTTGCAGCC
bb080109r1   50-80   GGCGGCCGCTCTAGAAACTAGTGGATCCCCC
bc070109f1   11-26   CGAAATCCTGCAGCCC
bd010109r1   15-49   CGGGGGGCGGCCGCTCTAGAACTAGTGGATCCCCC
bd090109r1   15-48   GGTGGCGGCCGCTCTAGAACTAGTTGGATCCCCC
bf120109f1    1-22   AAAAATAACGAATTCTGCAGCC
bg040109f1    2-25   AAAATGAATCGGAATTCTGCAGCC
bh120109f1   20-30   ATTCTGCAGCC
c03hba0049i23_sp601  8- 8   C
c03hba0049i23_sp603  9- 9   C
ca070109f1   25-42   TATCGAATTCTGCAGCCC
cb120109f1   13-26   CGAATCCTGCAGCC
cb120109r1   11-52   TCCCGGCGGTGGGCGGCCGCTCTAAGACTAGTGGGATCCCCC
cc080109f1   44-56   CTGCAGCCCCTTC
cc080109r1   22-56   TGGGCGTGCCGCTCTTAGAACTAGTTGGATCCCCC
cc100109f1   10-23   CGAATCCTGCAGCC
cc100109r1    9-50   TCCCGGCGGGGGGCGGCCGCTCTAGAACTATGTGGATCCCCC
cd020109f1   20-21   CC
ce090109f1   14-23   TCTGCAGCCC
cf080109f1   10-27   ATCGAAATTCCTGCAGCC
cf090109f1    8-28   TAACGAATCCTGCAGCCCTTC
cf090109r1   15-47   TGGGCGGCCGCTCTAGAACTAGTGGGATCCCCC
cf100109r1   10-49   CCCGCGGGTGGCGGGCGCTCTAGAACTAGTTGGATCCCCC
cg080109f1   10-25   CGAATTCCTGCAGCCC
cg090109f1    2-25   AAAAATGAACGAATTCCTGCAGCC
cg110109f1   11-26   CGAATTCTTGCAGCCC
ch040109r1   20-53   CGGGGGGCGGCTGCTCTAGAACTAGTGGATCCCC
ch080109r1   21-51   GGCGGCCGCTCTAGAAACTAGTGGATCCCCC
da070109f1    8-23   TATCGATTCTGCAGCC
dc080109r1   16-51   CGGGTGGCGGCCGCTCTAGAACTAGTTGGATCCCCC
dc110109f1   20-35   CGAATTCCTGCAGCCC
dd100109r1    1-45   GTGTGAACCCTCGCGGGTGGCGGCCGCTCTAGACTAGTGGACCCC
de070109r1   10-48   CCGTGGTGGCGGCCGCTCTAGAACTAGTTGGATCCCCCT
de080109f1   12-20   TCTGCGCCC
df060109r1   15-51   CGGGTGGCGGCCGCTCTAGTAACTAGTTGGATCCCCC
df070109f1   30-31   CC
dh030109f1   33-41   CTGCAGCCC
dh040109r1   15-47   GGTGGCGGCCGCTCTAGAACTAGTTGGATCCCC
dh110109r1    8-47   CCCGCGGGTGGCGGCCGCTCTAGAACTAGTTGGATCCCCC
ea010109f1   16-26   TTCCTGCAGCC
ea110109f1    1-24   AAAATGAAATCGATTCCTGCAGCC
eb070109f1   13-27   CGAATTCCTGCAGCC
eb090109f1   25-26   CC
ec120109r1   46-49   CCCC
ed020109r1   14-47   CGGGGGGCGGCCGCTCTAGAACTAGTGGATCCCC
ed070109f1    1-25   AAAATGAATCGAAATCCTGCAGCCC
ef090109f1    9-24   CGAATTCCTGGCAGCC
ef110109r1    8-47   CTCCCGCCGGGTGGCGGCCGCTCTAGAACTAGTGGTCCCC
eg050109r1   10-52   CCCCGCCGGTTGGGCGGCCGCTCTAGAAACTAGTGGATCCCCC
eg080109f1   10-12   CGG
eg110109f1   14-16   CGG
eh030109f1    7-27   AACGAATTCCTGCAGCCCTCC

Near duplicate reads: 
ae110109f1            eh030109f1      (imperfect: 6-963 (27)   6-966 (5) )
ae120109f1            ed070109f1      (imperfect: 10-1005 (12)   9-987 (1) )
bc070109f1            cg110109f1      (imperfect: 10-1004 (9)   10-1007 (0) )
bc070109r1            cg110109r1      (imperfect: 49-1013 (29)   49-1014 (0) )
bd110109r1            ch090109r1      (imperfect: 49-1016 (2)   48-1012 (0) )
be070109f1            cg060109f1      (imperfect: 10-1037 (16)   12-1023 (24) )
be100109f1            ce120109f1      (imperfect: 21-988 (15)   28-995 (6) )
bg110109r1            dg110109r1      (imperfect: 7-986 (8)   8-997 (13) )
c03hba0049i23_sp601       c03hba0049i23_sp602 (imperfect: 8-968 (10)   11-960 (8) )
c03hba0049i23_sp602       c03hba0049i23_sp603 (imperfect: 19-938 (30)   15-936 (20) )
cb120109f1            cc100109f1      (imperfect: 12-977 (0)   9-970 (43) )
cb120109r1            cc100109r1      (imperfect: 10-981 (3)   8-981 (42) )
ce040109r1            de040109r1      (imperfect: 10-1053 (5)   8-1031 (5) )
ch060109f1            db110109f1      (imperfect: 37-985 (33)   29-978 (17) )
ea090109r1            ed070109r1      (imperfect: 47-956 (0)   49-957 (20) )
ea110109f1            ed070109f1      (imperfect: 0-956 (0)   0-950 (38) )
eb070109f1            ef090109f1      (imperfect: 12-988 (14)   8-985 (5) )
eb070109r1            ef090109r1      (imperfect: 47-970 (8)   49-978 (3) )

Internal read matches (same orientation) : 
229   aa050109r1    tandem (268-mer)_2    434-1072 
137   ac020109f1    tandem (41-mer)_7    148-464 
143   ac020109f1    tandem (75-mer)_3    165-464 
119   ac020109f1    tandem (116-mer)_2    137-464 
 37   ac020109f1    disjoint 75-mers  165-239 / 391-464 
151   ac120109r1    tandem (37-mer)_8    124-454 
148   ac120109r1    tandem (74-mer)_4    124-422 
131   ac120109r1    tandem (111-mer)_2    124-450 
 87   ac120109r1    tandem (148-mer)_2    124-422 
 74   ac120109r1    disjoint 138-mers  124-261 / 311-454 
 47   ac120109r1    disjoint 101-mers  124-224 / 349-454 
138   ad120109r1    disjoint 161-mers  122-282 / 390-550 
152   af100109f1    tandem (37-mer)_8    253-584 
149   af100109f1    tandem (74-mer)_4    253-552 
132   af100109f1    tandem (111-mer)_2    253-580 
 87   af100109f1    tandem (148-mer)_2    253-552 
 74   af100109f1    disjoint 139-mers  253-391 / 440-584 
 48   af100109f1    disjoint 102-mers  253-354 / 478-584 
 99   ag020109r1    disjoint 110-mers  50-159 / 318-427 
 34   ag080109f1    tandem (95-mer)_2    754-957 
151   ah110109f1    tandem (41-mer)_8    444-775 
149   ah110109f1    tandem (75-mer)_3    476-775 
132   ah110109f1    tandem (116-mer)_2    448-775 
 88   ah110109f1    tandem (152-mer)_1    476-775 
 47   ah110109f1    disjoint 107-mers  444-550 / 674-775 
105   ba010109f1    tandem (75-mer)_3    653-887 
 54   ba070109r1    tandem (94-mer)_2    249-464 
255   bc040109f1    tandem (268-mer)_2     25-581 
258   bf050109r1    tandem (268-mer)_2     50-608 
152   bf110109f1    tandem (37-mer)_8    129-460 
149   bf110109f1    tandem (74-mer)_4    129-428 
132   bf110109f1    tandem (111-mer)_2    129-456 
 87   bf110109f1    tandem (148-mer)_2    129-428 
 74   bf110109f1    disjoint 139-mers  129-267 / 316-460 
 48   bf110109f1    disjoint 102-mers  129-230 / 354-460 
 54   bg050109r1    tandem (94-mer)_2    475-690 
129   bh020109f1    tandem (41-mer)_8    451-779 
120   bh020109f1    tandem (75-mer)_3    483-780 
151   bh060109f1    tandem (41-mer)_8    123-454 
149   bh060109f1    tandem (75-mer)_3    155-454 
132   bh060109f1    tandem (116-mer)_2    127-454 
 88   bh060109f1    tandem (152-mer)_1    155-454 
 47   bh060109f1    disjoint 107-mers  123-229 / 353-454 
364   ca040109f1    tandem (272-mer)_2    213-995 
127   ca040109f1    disjoint 239-mers  213-451 / 753-995 
289   ca090109f1    tandem (269-mer)_2     28-629 
 43   ca090109f1    disjoint 66-mers  28-93 / 565-629 
151   cb010109f1    tandem (41-mer)_8    330-661 
149   cb010109f1    tandem (75-mer)_3    362-661 
132   cb010109f1    tandem (116-mer)_2    334-661 
 88   cb010109f1    tandem (152-mer)_1    362-661 
 47   cb010109f1    disjoint 107-mers  330-436 / 560-661 
351   cb050109r1    tandem (268-mer)_2    254-977 
117   cb050109r1    disjoint 178-mers  254-431 / 792-977 
136   cb080109f1    tandem (38-mer)_7     59-353 
142   cb080109f1    tandem (75-mer)_3     54-353 
115   cb080109f1    tandem (114-mer)_2     28-353 
 81   cb080109f1    tandem (152-mer)_1     54-353 
 36   cb080109f1    disjoint 75-mers  54-128 / 280-353 
151   cd050109f1    tandem (41-mer)_8    416-747 
149   cd050109f1    tandem (75-mer)_3    448-747 
132   cd050109f1    tandem (116-mer)_2    420-747 
 88   cd050109f1    tandem (152-mer)_1    448-747 
 47   cd050109f1    disjoint 107-mers  416-522 / 646-747 
122   cg040109f1    tandem (41-mer)_7    620-938 
116   cg040109f1    tandem (75-mer)_3    652-920 
102   cg040109f1    tandem (116-mer)_2    624-920 
432   dd040109f1    tandem (268-mer)_2     89-884 
189   dd040109f1    disjoint 254-mers  89-342 / 625-884 
 33   dd060109f1    disjoint 49-mers  105-153 / 373-421 
330   dd120109r1    tandem (268-mer)_2    236-981 
 94   dd120109r1    disjoint 194-mers  236-429 / 773-981 
 52   df010109f1    tandem (94-mer)_2    117-332 
152   dh060109f1    tandem (37-mer)_8    298-629 
149   dh060109f1    tandem (74-mer)_4    298-597 
132   dh060109f1    tandem (111-mer)_2    298-625 
 87   dh060109f1    tandem (148-mer)_2    298-597 
 74   dh060109f1    disjoint 139-mers  298-436 / 485-629 
 48   dh060109f1    disjoint 102-mers  298-399 / 523-629 
 45   eb040109r1    disjoint 51-mers  45-95 / 313-363 
 38   ed100109f1    disjoint 81-mers  33-113 / 127-210 
 54   ee020109r1    tandem (97-mer)_2    606-821 
151   ef110109f1    tandem (41-mer)_8    378-709 
149   ef110109f1    tandem (75-mer)_3    410-709 
132   ef110109f1    tandem (116-mer)_2    382-709 
 88   ef110109f1    tandem (152-mer)_1    410-709 
 47   ef110109f1    disjoint 107-mers  378-484 / 608-709 
147   eh040109f1    tandem (41-mer)_7    177-500 
141   eh040109f1    tandem (75-mer)_3    209-497 
124   eh040109f1    tandem (116-mer)_2    181-497 
 39   eh040109f1    disjoint 99-mers  177-275 / 407-500 
131   eh040109r1    tandem (39-mer)_8     47-373 
120   eh040109r1    tandem (77-mer)_3     50-341 
111   eh040109r1    tandem (113-mer)_2     62-369 
 53   eh040109r1    disjoint 131-mers  50-180 / 241-373 
152   eh070109r1    tandem (37-mer)_8    279-610 
149   eh070109r1    tandem (74-mer)_4    279-578 
132   eh070109r1    tandem (111-mer)_2    279-606 
 87   eh070109r1    tandem (148-mer)_2    279-578 
 74   eh070109r1    disjoint 139-mers  279-417 / 466-610 
 48   eh070109r1    disjoint 102-mers  279-380 / 504-610 

No. of node-rejected pairs: None.

Multi-segment reads (initially rejected segments in parentheses) -- XXX means segments flank X'd region: 
ab040109r1          (5 86)  82 930 
ac050109r1          (99 163)  164 1074 
ad010109r1          (27 58)  62 118 
ad090109r1          (87 165)  164 1125 
ae030109r1          (1 45)  48 307 
ae120109r1          (115 150)  147 1091 
af010109r1          (51 114)  397 641 
ag040109f1    XXX   16 174  (881 936) 
ag100109r1          (11 53)  48 978 
ah100109r1          (67 147)  145 1028 
ba120109r1          (1 62)  66 905 
bd090109r1          (15 51)  49 1022 
bd100109r1          49 658  (676 1037) 
cc060109r1          (40 118)  116 1026 
cd110109r1          (111 148)  148 1144 
ch080109r1          (21 51)  52 1021 
da100109r1          (9 46)  46 1009 
dc080109r1          (16 51)  52 991 
dd020109r1          53 471  (527 1003) 
dd100109f1    XXX   14 280  (991 1045) 
dd100109r1          (1 46)  46 313 
de030109r1          280 516  (746 980) 
de070109r1          (10 48)  49 574 
dg010109r1          (16 50)  47 534 
dh040109r1          (15 49)  48 938 
eb120109r1          (50 401)  595 945 
ec020109f1          26 683  (739 887) 

27 reads with multiple segments.

Probable deletion reads (excluded from assembly):

ag100109r1    14    46- 53  (  dc080109r1     51- 72)

1 probable deletion reads.


Revised quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90  461770  45.0  461770  45.0    0.00
 89     863   0.1  462633  45.1    0.00
 88     799   0.1  463432  45.1    0.00
 87     835   0.1  464267  45.2    0.00
 86     572   0.1  464839  45.3    0.00
 85     731   0.1  465570  45.3    0.00
 84     705   0.1  466275  45.4    0.00
 83     488   0.0  466763  45.5    0.00
 82     555   0.1  467318  45.5    0.00
 81    3485   0.3  470803  45.8    0.00
 80     225   0.0  471028  45.9    0.00
 79     403   0.0  471431  45.9    0.00
 78     382   0.0  471813  45.9    0.00
 77     284   0.0  472097  46.0    0.00
 76     858   0.1  472955  46.1    0.00
 75     435   0.0  473390  46.1    0.00
 74     204   0.0  473594  46.1    0.00
 73     360   0.0  473954  46.2    0.00
 72     222   0.0  474176  46.2    0.00
 71     356   0.0  474532  46.2    0.00
 70     156   0.0  474688  46.2    0.00
 69     319   0.0  475007  46.3    0.00
 68     213   0.0  475220  46.3    0.00
 67     399   0.0  475619  46.3    0.00
 66   22042   2.1  497661  48.5    0.01
 65    1256   0.1  498917  48.6    0.01
 64     126   0.0  499043  48.6    0.01
 63      93   0.0  499136  48.6    0.01
 62     319   0.0  499455  48.6    0.01
 61    3525   0.3  502980  49.0    0.01
 60    1678   0.2  504658  49.1    0.01
 59     312   0.0  504970  49.2    0.01
 58     437   0.0  505407  49.2    0.01
 57     693   0.1  506100  49.3    0.01
 56    3871   0.4  509971  49.7    0.02
 55     412   0.0  510383  49.7    0.03
 54    1874   0.2  512257  49.9    0.03
 53     931   0.1  513188  50.0    0.04
 52    2208   0.2  515396  50.2    0.05
 51    1010   0.1  516406  50.3    0.06
 50    1784   0.2  518190  50.5    0.08
 49     599   0.1  518789  50.5    0.08
 48     644   0.1  519433  50.6    0.09
 47     845   0.1  520278  50.7    0.11
 46     816   0.1  521094  50.7    0.13
 45    1008   0.1  522102  50.8    0.16
 44    1470   0.1  523572  51.0    0.22
 43    1045   0.1  524617  51.1    0.27
 42    1838   0.2  526455  51.3    0.39
 41     999   0.1  527454  51.4    0.47
 40   20098   2.0  547552  53.3    2.48
 39     412   0.0  547964  53.4    2.53
 38     285   0.0  548249  53.4    2.58
 37     602   0.1  548851  53.4    2.70
 36     309   0.0  549160  53.5    2.77
 35     713   0.1  549873  53.5    3.00
 34     719   0.1  550592  53.6    3.29
 33     707   0.1  551299  53.7    3.64
 32     549   0.1  551848  53.7    3.99
 31     371   0.0  552219  53.8    4.28
 30     279   0.0  552498  53.8    4.56
 29     654   0.1  553152  53.9    5.38
 28     264   0.0  553416  53.9    5.80
 27     465   0.0  553881  53.9    6.73
 26     305   0.0  554186  54.0    7.50
 25    2368   0.2  556554  54.2   14.98
 24     691   0.1  557245  54.3   17.74
 23     595   0.1  557840  54.3   20.72
 22     418   0.0  558258  54.4   23.36
 21     553   0.1  558811  54.4   27.75
 20     391   0.0  559202  54.5   31.66
 19     641   0.1  559843  54.5   39.73
 18     373   0.0  560216  54.6   45.64
 17     485   0.0  560701  54.6   55.32
 16     608   0.1  561309  54.7   70.59
 15     863   0.1  562172  54.7   97.88
 14     614   0.1  562786  54.8  122.32
 13     859   0.1  563645  54.9  165.37
 12     743   0.1  564388  55.0  212.25
 11    1232   0.1  565620  55.1  310.12
 10    1651   0.2  567271  55.2  475.22
  9    2232   0.2  569503  55.5  756.21
  8    1724   0.2  571227  55.6  1029.44
  7    1447   0.1  572674  55.8  1318.16
  6     757   0.1  573431  55.8  1508.31
  5      43   0.0  573474  55.8  1521.91
  4     138   0.0  573612  55.9  1576.84
  3      76   0.0  573688  55.9  1614.93
  2  161575  15.7  735263  71.6  103561.87
  0    8934   0.9  744197  72.5  112495.87
 -1  282716  27.5  1026913 100.0  395211.87   (quality -1 = terminal quality 0)

Avg. full length: 1063.1, trimmed (qual > -1): 770.4
Avg. quality: 46.1 per base

LLR score histogram:
Score    #   cum # 
-95.0  2820  2820
-90.0    28  2848
-85.0     9  2857
-80.0     8  2865
-75.0    10  2875
-70.0     7  2882
-65.0    10  2892
-60.0    12  2904
-55.0     7  2911
-50.0    30  2941
-45.0     6  2947
-40.0    15  2962
-35.0    19  2981
-30.0    16  2997
-25.0    45  3042
-20.0    16  3058
-15.0    24  3082
-10.0    53  3135
 -5.0    44  3179
  0.0  1939  5118
  5.0  2074  7192
 10.0  1953  9145
 15.0  1466  10611
 20.0    80  10691

LLR score histogram:
Score    #   cum # 
-95.0  2819  2819
-90.0    29  2848
-85.0     9  2857
-80.0     8  2865
-75.0     9  2874
-70.0     8  2882
-65.0    10  2892
-60.0    11  2903
-55.0     7  2910
-50.0    32  2942
-45.0     4  2946
-40.0    16  2962
-35.0    18  2980
-30.0    16  2996
-25.0    46  3042
-20.0    17  3059
-15.0    22  3081
-10.0    54  3135
 -5.0    44  3179
  0.0  1911  5090
  5.0  2061  7151
 10.0  1964  9115
 15.0  1493  10608
 20.0    83  10691

2d revised quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90  460869  44.9  460869  44.9    0.00
 89     887   0.1  461756  45.0    0.00
 88     830   0.1  462586  45.0    0.00
 87     866   0.1  463452  45.1    0.00
 86     624   0.1  464076  45.2    0.00
 85     773   0.1  464849  45.3    0.00
 84     727   0.1  465576  45.3    0.00
 83     494   0.0  466070  45.4    0.00
 82     562   0.1  466632  45.4    0.00
 81    3250   0.3  469882  45.8    0.00
 80     245   0.0  470127  45.8    0.00
 79     411   0.0  470538  45.8    0.00
 78     385   0.0  470923  45.9    0.00
 77     310   0.0  471233  45.9    0.00
 76     827   0.1  472060  46.0    0.00
 75     438   0.0  472498  46.0    0.00
 74     208   0.0  472706  46.0    0.00
 73     358   0.0  473064  46.1    0.00
 72     229   0.0  473293  46.1    0.00
 71     365   0.0  473658  46.1    0.00
 70     149   0.0  473807  46.1    0.00
 69     322   0.0  474129  46.2    0.00
 68     217   0.0  474346  46.2    0.00
 67     397   0.0  474743  46.2    0.00
 66   22586   2.2  497329  48.4    0.01
 65    1230   0.1  498559  48.5    0.01
 64     128   0.0  498687  48.6    0.01
 63      95   0.0  498782  48.6    0.01
 62     322   0.0  499104  48.6    0.01
 61    3576   0.3  502680  49.0    0.01
 60    1683   0.2  504363  49.1    0.01
 59     310   0.0  504673  49.1    0.01
 58     444   0.0  505117  49.2    0.01
 57     695   0.1  505812  49.3    0.01
 56    3992   0.4  509804  49.6    0.02
 55     440   0.0  510244  49.7    0.03
 54    1870   0.2  512114  49.9    0.03
 53     932   0.1  513046  50.0    0.04
 52    2206   0.2  515252  50.2    0.05
 51    1033   0.1  516285  50.3    0.06
 50    1814   0.2  518099  50.5    0.08
 49     601   0.1  518700  50.5    0.09
 48     645   0.1  519345  50.6    0.10
 47     845   0.1  520190  50.7    0.11
 46     815   0.1  521005  50.7    0.13
 45    1003   0.1  522008  50.8    0.16
 44    1474   0.1  523482  51.0    0.22
 43    1053   0.1  524535  51.1    0.28
 42    1854   0.2  526389  51.3    0.39
 41     988   0.1  527377  51.4    0.47
 40   20036   2.0  547413  53.3    2.48
 39     417   0.0  547830  53.3    2.53
 38     288   0.0  548118  53.4    2.57
 37     607   0.1  548725  53.4    2.69
 36     302   0.0  549027  53.5    2.77
 35     716   0.1  549743  53.5    3.00
 34     717   0.1  550460  53.6    3.28
 33     699   0.1  551159  53.7    3.63
 32     542   0.1  551701  53.7    3.97
 31     372   0.0  552073  53.8    4.27
 30     283   0.0  552356  53.8    4.55
 29     647   0.1  553003  53.9    5.37
 28     268   0.0  553271  53.9    5.79
 27     469   0.0  553740  53.9    6.73
 26     307   0.0  554047  54.0    7.50
 25    2378   0.2  556425  54.2   15.02
 24     693   0.1  557118  54.3   17.78
 23     595   0.1  557713  54.3   20.76
 22     417   0.0  558130  54.4   23.39
 21     554   0.1  558684  54.4   27.79
 20     408   0.0  559092  54.4   31.87
 19     648   0.1  559740  54.5   40.03
 18     375   0.0  560115  54.5   45.97
 17     494   0.0  560609  54.6   55.83
 16     613   0.1  561222  54.7   71.23
 15     878   0.1  562100  54.7   98.99
 14     627   0.1  562727  54.8  123.95
 13     875   0.1  563602  54.9  167.81
 12     759   0.1  564361  55.0  215.70
 11    1250   0.1  565611  55.1  314.99
 10    1663   0.2  567274  55.2  481.29
  9    2307   0.2  569581  55.5  771.72
  8    1731   0.2  571312  55.6  1046.07
  7    1543   0.2  572855  55.8  1353.94
  6     776   0.1  573631  55.9  1548.86
  5     150   0.0  573781  55.9  1596.29
  4     299   0.0  574080  55.9  1715.33
  3     239   0.0  574319  55.9  1835.11
  2  160944  15.7  735263  71.6  103383.91
  0    8934   0.9  744197  72.5  112317.91
 -1  282716  27.5  1026913 100.0  395033.91   (quality -1 = terminal quality 0)

Avg. full length: 1063.1, trimmed (qual > -1): 770.4
Avg. quality: 46.1 per base

No. confirmed reads: 722
Avg. length: 1034.6, confirmed: 837.0, str. confirmed: 791.8, trimmed: 883.1
Preliminary clone size estimate: 58155 bp, depth of coverage: 10.4

Depth histogram (max_depth, #reads, cum #reads):

25    51      51
24     5      56
23     4      60
22     6      66
21    27      93
20    36     129
19    54     183
18    67     250
17    79     329
16    25     354
15    35     389
14    26     415
13    53     468
12    51     519
11    45     564
10    32     596
 9    30     626
 8    35     661
 7     6     667
 6     4     671
 5    19     690
 4     8     698
 3     6     704
 2     3     707
 1    15     722
 0   243     965

Forward confirmed bases: 0

Substitutions by nucleotide:
       A      C      G      T      N      X      Z    Total
A      0      0      0      0      0      0      0        0
C      0      0      0      0      0      0      0        0
G      0      0      0      0      0      0      0        0
T      0      0      0      0      0      0      0        0
N      0      0      0      0      0      0      0        0
X      0      0      0      0      0      0      0        0
Z      0      0      0      0      0      0      0        0

Substitutions by quality: 
       Total

Histogram of spacings between adjacent indel pairs:


Reverse confirmed bases: 0

Substitutions by nucleotide:
       A      C      G      T      N      X      Z    Total
A      0      0      0      0      0      0      0        0
C      0      0      0      0      0      0      0        0
G      0      0      0      0      0      0      0        0
T      0      0      0      0      0      0      0        0
N      0      0      0      0      0      0      0        0
X      0      0      0      0      0      0      0        0
Z      0      0      0      0      0      0      0        0

Substitutions by quality: 
       Total

Histogram of spacings between adjacent indel pairs:


Blocked reads: 
ad010109r1 98 133   right
ad050109f1 33 775  left 
ae030109r1 45 317  left right
ag040109r1 53 214   right
ah020109r1 466 744  left right
ba040109r1 131 171  left 
bd030109r1 48 555   right
be070109f1 20 788  left 
be070109r1 45 569  left 
bf060109f1 151 371   right
bg110109f1 41 746  left right
bg110109r1 19 754  left right
cb020109r1 27 759  left 
cc090109r1 49 410   right
cd010109f1 80 787  left 
ce040109f1 39 765   right
ce080109f1 529 786  left 
cf040109r1 49 640   right
cg050109r1 46 657   right
cg060109f1 26 849   right
cg060109r1 52 611  left right
ch070109r1 65 90  left right
da090109r1 141 872  left 
da100109r1 18 750  left 
dd100109r1 45 312   right
dd110109r1 48 612   right
de040109f1 25 753  left right
de040109r1 39 778  left right
de070109r1 48 580   right
eb100109r1 80 782  left 
ec070109r1 50 378   right
ee060109r1 80 829  left 
eg080109r1 48 282   right
eg110109r1 49 283   right
eh040109r1 86 543   right

35 blocked reads: 11 left only, 16 right only, 8 both.
20 reads (not shown) lack a high-quality segment.
Bypassed reads: da040109r1 cg050109r1
Bypassed reads:  eh040109r1
UNPOSITIONED READ: ch070109r1
UNPOSITIONED READ: ac030109r1
UNPOSITIONED READ: bd010109r1

0 perfect duplicates

230 isolated singletons (having no non-vector match to any other read): 
  Read         Length      (# trimmed non-X bases)
 db030109r1    1050   (0)
 db040109f1    1075   (0)
 db040109r1    1062   (0)
 db050109f1    1106   (663)
 db050109r1    1071   (683)
 db060109r1    1200   (0)
 db030109f1    1048   (0)
 da080109f1    1153   (0)
 da080109r1    1066   (0)
 da110109r1    1021   (0)
 da120109f1    1081   (0)
 da120109r1     977   (0)
 db010109r1    1526   (0)
 db020109r1    1101   (0)
 dc040109f1    1107   (0)
 de010109r1    1675   (0)
 de120109f1    1013   (0)
 de120109r1    1073   (47)
 df050109f1    1076   (0)
 df050109r1    1147   (0)
 df060109f1    1084   (0)
 dd080109r1    1053   (0)
 dc040109r1    1763   (0)
 dc060109f1    1118   (0)
 dc070109f1    1181   (0)
 dc070109r1    1166   (0)
 dc110109r1    1022   (0)
 dd010109r1    1523   (0)
 dd080109f1    1069   (0)
 da050109r1    1525   (0)
 cf050109r1    1037   (707)
 cf060109f1    1135   (0)
 cf060109r1    1073   (0)
 cf070109f1    1059   (0)
 cf070109r1    1124   (0)
 cf100109f1    1030   (0)
 cf050109f1    1044   (633)
 cc050109r1    1078   (0)
 cc110109f1    1009   (0)
 cd020109r1    2454   (0)
 cd080109r1    1116   (0)
 cd090109f1    1055   (0)
 cd090109r1    1032   (0)
 ce030109r1    1086   (0)
 cf120109r1    1571   (0)
 ch120109f1    1100   (0)
 ch120109r1    1098   (0)
 da010109r1    1609   (0)
 da020109f1    1033   (0)
 da020109r1    1041   (0)
 da050109f1    1618   (0)
 ch100109r1    1036   (0)
 cg020109f1    1015   (0)
 cg020109r1    1034   (0)
 cg070109r1    2718   (0)
 cg080109r1    1178   (0)
 ch040109f1    1064   (0)
 ch070109f1    1041   (0)
 ch100109f1    1018   (0)
 df080109f1    1268   (110)
 ef050109r1    1085   (0)
 ef060109r1    1044   (0)
 ef080109r1    1006   (0)
 ef100109r1    1100   (31)
 ef120109f1    1541   (0)
 ef120109r1     933   (0)
 ef050109f1    1002   (0)
 ee090109f1    1520   (0)
 ee090109r1     993   (0)
 ee100109f1     975   (754)
 ee100109r1     977   (710)
 ee120109r1     964   (0)
 ef040109f1     979   (0)
 ef040109r1     986   (0)
 eg010109r1    1514   (0)
 eh080109f1     981   (0)
 eh080109r1     971   (0)
 eh090109f1     987   (0)
 eh090109r1     966   (0)
 eh100109f1     952   (0)
 eh100109r1    1058   (0)
 eh050109r1    1396   (0)
 eg030109f1     979   (0)
 eg030109r1     960   (0)
 eg050109f1    1004   (0)
 eg060109r1    1000   (0)
 eg070109f1    1076   (0)
 eg070109r1    1508   (0)
 eh050109f1     996   (49)
 ed080109r1    1123   (0)
 dh010109r1    1420   (0)
 dh020109f1    1419   (0)
 dh020109r1    1464   (0)
 dh080109r1    1985   (0)
 dh090109r1    1708   (0)
 dh110109f1    1011   (0)
 dh010109f1    1018   (0)
 df080109r1    1150   (535)
 dg020109f1    1018   (0)
 dg020109r1    1020   (0)
 dg070109f1    1120   (0)
 dg070109r1    2298   (0)
 dg090109f1    1147   (0)
 dg090109r1    1325   (0)
 ea050109f1     984   (0)
 ec010109r1    1818   (0)
 ec090109f1    1430   (0)
 ec110109f1    1246   (0)
 ec110109r1     969   (0)
 ed050109f1     994   (0)
 ed050109r1    1010   (0)
 ec010109f1    1014   (0)
 ea050109r1     990   (0)
 ea120109f1     927   (0)
 ea120109r1    1373   (0)
 eb010109f1     975   (0)
 eb010109r1     965   (0)
 eb080109f1    1007   (0)
 eb080109r1    1032   (0)
 cc110109r1    1073   (0)
 af120109r1     998   (0)
 ag050109f1    1050   (0)
 ag050109r1    1053   (0)
 ag110109r1    1198   (0)
 ah010109f1     965   (0)
 ah010109r1    1003   (0)
 af120109f1     991   (0)
 ae080109r1    1198   (0)
 af050109r1    1046   (0)
 af070109r1    1071   (42)
 af080109f1    1205   (0)
 af080109r1    1179   (0)
 af090109f1    1027   (0)
 af090109r1    1012   (0)
 ah030109f1    1032   (0)
 ba080109r1    1135   (8)
 bb010109f1    1016   (156)
 bb010109r1    1089   (0)
 bb030109f1    1049   (0)
 bb070109f1    1020   (0)
 bb070109r1    1037   (0)
 ba040109f1    1033   (0)
 ah030109r1    1024   (0)
 ah060109r1    1055   (0)
 ah080109r1    1128   (0)
 ah090109f1    1122   (3)
 ah090109r1    1131   (8)
 ba020109f1    1032   (0)
 ba020109r1    1036   (0)
 ae080109f1    2983   (0)
 aa090109r1    1027   (0)
 aa100109r1    1967   (0)
 aa120109r1    1057   (0)
 ab010109f1     999   (0)
 ab010109r1    1018   (0)
 ab070109f1    1391   (0)
 aa090109f1    1167   (0)
 aa030109f1    1095   (0)
 aa030109r1    1040   (0)
 aa040109f1    1067   (0)
 aa040109r1    1046   (0)
 aa060109f1    1119   (0)
 aa060109r1    1140   (0)
 aa080109r1    1181   (8)
 ab070109r1    1661   (0)
 ac060109f1    1126   (0)
 ac070109f1    1114   (0)
 ac070109r1    2445   (0)
 ad020109f1    1023   (0)
 ad020109r1    1194   (40)
 ad100109f1    1044   (0)
 ad100109r1    1166   (0)
 ac040109r1    1067   (645)
 ab090109f1    1112   (1)
 ab120109f1     992   (0)
 ab120109r1     981   (0)
 ac010109f1    1050   (0)
 ac010109r1    1034   (0)
 ac030109f1    1047   (0)
 ac040109f1    1084   (676)
 bb030109r1    1038   (0)
 bf080109r1    1075   (0)
 bf120109r1    1036   (0)
 bg010109r1    1544   (0)
 bg060109f1    1045   (0)
 bg060109r1    1036   (0)
 bf080109f1    1060   (0)
 be020109r1    1060   (0)
 be110109f1    1006   (0)
 be120109r1    1006   (0)
 bf020109r1    1068   (33)
 bf040109r1    1051   (0)
 bf060109r1    1250   (0)
 bh040109f1    1005   (0)
 cb030109r1    1052   (34)
 cb100109f1    1053   (0)
 cb100109r1    1027   (0)
 cc010109f1    1044   (0)
 cc010109r1    1051   (0)
 cc050109f1    1080   (0)
 ca120109r1     971   (0)
 bh040109r1    1042   (0)
 bh110109f1    1048   (0)
 bh110109r1    1098   (0)
 bh120109r1    1049   (0)
 ca060109r1    1099   (0)
 ca120109f1     964   (0)
 bf040109f1    1042   (0)
 bd010109f1     996   (0)
 bd020109f1    1002   (0)
 bd020109r1    1036   (0)
 bd040109f1    1062   (710)
 bd040109r1    1079   (683)
 bd060109f1    1047   (0)
 bc100109r1    1016   (0)
 bb080109f1    1039   (0)
 bb090109r1    1093   (0)
 bb110109f1     979   (0)
 bb110109r1    1010   (0)
 bc090109f1    1016   (0)
 bc090109r1    1031   (0)
 bc100109f1    1004   (0)
 be020109f1    1028   (0)
 bd070109r1    1057   (0)
 bd080109r1    1043   (0)
 bd120109f1    1008   (0)
 bd120109r1    1001   (0)
 bd080109f1    1046   (0)
 bd060109r1    2439   (0)
 bd070109f1    1050   (0)

Contig 1.  1 read; 1024 bp (untrimmed), 756 (trimmed).
 ****  PROBABLE DELETION READ
      1  1024 ag100109r1   1009 (825)  0.10 0.00 0.00    0 (1024)    0 (1023) 

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56     324  31.6     324  31.6    0.00
 51     105  10.3     429  41.9    0.00
 50       9   0.9     438  42.8    0.00
 48       3   0.3     441  43.1    0.00
 46       4   0.4     445  43.5    0.00
 45      31   3.0     476  46.5    0.00
 44       6   0.6     482  47.1    0.00
 43      14   1.4     496  48.4    0.00
 42      12   1.2     508  49.6    0.00
 40      56   5.5     564  55.1    0.01
 39       3   0.3     567  55.4    0.01
 37       6   0.6     573  56.0    0.01
 36       1   0.1     574  56.1    0.01
 35      15   1.5     589  57.5    0.02
 34       8   0.8     597  58.3    0.02
 33       6   0.6     603  58.9    0.02
 32      11   1.1     614  60.0    0.03
 31       7   0.7     621  60.6    0.04
 30       1   0.1     622  60.7    0.04
 29       9   0.9     631  61.6    0.05
 28       8   0.8     639  62.4    0.06
 27      12   1.2     651  63.6    0.08
 26       2   0.2     653  63.8    0.09
 25      11   1.1     664  64.8    0.12
 24       4   0.4     668  65.2    0.14
 23       4   0.4     672  65.6    0.16
 22       5   0.5     677  66.1    0.19
 21       6   0.6     683  66.7    0.24
 20       5   0.5     688  67.2    0.29
 19      11   1.1     699  68.3    0.43
 18       5   0.5     704  68.8    0.51
 17       5   0.5     709  69.2    0.61
 16       3   0.3     712  69.5    0.68
 15       9   0.9     721  70.4    0.97
 14       4   0.4     725  70.8    1.13
 13       1   0.1     726  70.9    1.18
 12      10   1.0     736  71.9    1.81
 11       3   0.3     739  72.2    2.05
 10       4   0.4     743  72.6    2.45
  9       6   0.6     749  73.1    3.20
  7       7   0.7     756  73.8    4.60
 -1     268  26.2    1024 100.0  272.60   (quality -1 = terminal quality 0)

Avg. full length: 1024.0, trimmed (qual > -1): 756.0
Avg. quality: 33.0 per base

Initial, terminal qual 0 segments:  1-50, 807-1024

Regions of LLR- adjusted quality < 2.0:
1-52, 75-83, 664-667, 687-689, 691, 700-703, 706-708, 727-736, 
744-749, 763-764, 767-773, 776-791, 794, 807-1024, 

14 regions, avg size 24.0, avg spacing 73.1

First_start: 1024, last_end: 1

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)     1- 1024 [16.8] (0,0)     ag100109r1         1-1024 | (11 53)  48 978 | DA:(**48 978**) || local(+/-) (0.0,0.0), distant (19.9,0.0)

Gaps in unique-read coverage:  None.

Contig 2.  1 read; 1049 bp (untrimmed), 125 (trimmed).
      1  1049 ag040109r1    213 (136)  0.00 0.00 0.00    0 (1049)  834 (1048) 

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56      21   2.0      21   2.0    0.00
 51       1   0.1      22   2.1    0.00
 48       1   0.1      23   2.2    0.00
 46       6   0.6      29   2.8    0.00
 44      14   1.3      43   4.1    0.00
 43       4   0.4      47   4.5    0.00
 42      32   3.1      79   7.5    0.00
 40       7   0.7      86   8.2    0.00
 39       2   0.2      88   8.4    0.00
 37       6   0.6      94   9.0    0.01
 35       1   0.1      95   9.1    0.01
 34       2   0.2      97   9.2    0.01
 33       4   0.4     101   9.6    0.01
 32       1   0.1     102   9.7    0.01
 30       3   0.3     105  10.0    0.01
 28       1   0.1     106  10.1    0.01
 27       4   0.4     110  10.5    0.02
 26       1   0.1     111  10.6    0.02
 24       1   0.1     112  10.7    0.03
 23       3   0.3     115  11.0    0.04
 18       3   0.3     118  11.2    0.09
 16       2   0.2     120  11.4    0.14
 15       1   0.1     121  11.5    0.17
 14       1   0.1     122  11.6    0.21
 13       1   0.1     123  11.7    0.26
 12       2   0.2     125  11.9    0.39
 -1     924  88.1    1049 100.0  924.39   (quality -1 = terminal quality 0)

Avg. full length: 1049.0, trimmed (qual > -1): 125.0
Avg. quality: 4.8 per base

Initial, terminal qual 0 segments:  1-90, 216-1049

Regions of LLR- adjusted quality < 2.0:
1-94, 118-123, 216-1049, 

3 regions, avg size 311.3, avg spacing 349.7

First_start: 1049, last_end: 1

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)     1-  215 [ 2.7] (0,0)     ag040109r1         1-215 | 54 214 | DA:(**54 214**) || local(+/-) (0.0,0.0), distant (2.9,0.0)

Gaps in unique-read coverage:  None.

Contig 3.  2 reads; 1053 bp (untrimmed), 871 (trimmed).  Isolated contig.
      1  1053 ce040109f1   1010 (  0)  0.66 0.00 0.19    0 ( 32)    0 (149) 
     15  1054 de040109f1    882 (  0)  2.44 0.29 0.78   14 ( 19)    3 (145) 

Overall discrep rates (%):             1.54 0.14 0.48

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 66     121  11.5     121  11.5    0.00
 61       7   0.7     128  12.2    0.00
 60     124  11.8     252  23.9    0.00
 58       1   0.1     253  24.0    0.00
 57      11   1.0     264  25.1    0.00
 56       4   0.4     268  25.5    0.00
 55       2   0.2     270  25.6    0.00
 54      78   7.4     348  33.0    0.00
 53      35   3.3     383  36.4    0.00
 52     124  11.8     507  48.1    0.00
 51       7   0.7     514  48.8    0.00
 50      35   3.3     549  52.1    0.00
 48       3   0.3     552  52.4    0.00
 47      30   2.8     582  55.3    0.00
 46       3   0.3     585  55.6    0.00
 45      21   2.0     606  57.5    0.00
 44      10   0.9     616  58.5    0.00
 43      10   0.9     626  59.4    0.00
 42       6   0.6     632  60.0    0.00
 41       7   0.7     639  60.7    0.01
 40       7   0.7     646  61.3    0.01
 39      12   1.1     658  62.5    0.01
 38       9   0.9     667  63.3    0.01
 37       9   0.9     676  64.2    0.01
 36       1   0.1     677  64.3    0.01
 35       7   0.7     684  65.0    0.01
 34       4   0.4     688  65.3    0.01
 33       3   0.3     691  65.6    0.02
 32       7   0.7     698  66.3    0.02
 31       6   0.6     704  66.9    0.03
 30       2   0.2     706  67.0    0.03
 29       7   0.7     713  67.7    0.04
 28       8   0.8     721  68.5    0.05
 27       5   0.5     726  68.9    0.06
 26       1   0.1     727  69.0    0.06
 25       2   0.2     729  69.2    0.07
 24       2   0.2     731  69.4    0.08
 23       1   0.1     732  69.5    0.08
 21       3   0.3     735  69.8    0.10
 20       8   0.8     743  70.6    0.18
 19       5   0.5     748  71.0    0.25
 18       1   0.1     749  71.1    0.26
 17       7   0.7     756  71.8    0.40
 16       3   0.3     759  72.1    0.48
 15      16   1.5     775  73.6    0.98
 14       8   0.8     783  74.4    1.30
 13      20   1.9     803  76.3    2.31
 12      13   1.2     816  77.5    3.13
 11       8   0.8     824  78.3    3.76
 10      11   1.0     835  79.3    4.86
  9      18   1.7     853  81.0    7.13
  8      12   1.1     865  82.1    9.03
  7       6   0.6     871  82.7   10.23
 -1     182  17.3    1053 100.0  192.23   (quality -1 = terminal quality 0)

Avg. full length: 1053.0, trimmed (qual > -1): 871.0
Avg. quality: 38.4 per base

Initial, terminal qual 0 segments:  1-32, 904-1053

Regions of LLR- adjusted quality < 2.0:
1-39, 92-98, 749, 756-758, 768-778, 784-789, 800-810, 813-816, 
819, 821-823, 825, 827, 829-830, 832-838, 840-861, 863-1053, 


16 regions, avg size 19.4, avg spacing 65.8

First_start: 33, last_end: 909

Slack, # used pairs (max_score), unused
 0     0  ( 0.0)     0 ( 0.0)        1
 2     1  (21.5)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 1054 - right        0+      de040109f1   (  15)    No           1038+

Bottom strand: 
 left - right     1053+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56    168    168   2030 (100.00)     0  0    0   0   0   0     0 (0.00)    0   44 (2.17)
51      7    175   1862 ( 91.72)     0  0    0   0   0   0     0 (0.00)    0   44 (2.36)
50    199    374   1855 ( 91.38)     0  0    0   0   0   0     0 (0.00)    0   44 (2.37)
48      1    375   1656 ( 81.58)     0  0    0   0   0   0     0 (0.00)    0   44 (2.66)
47     22    397   1655 ( 81.53)     0  0    0   0   0   0     0 (0.00)    0   44 (2.66)
46      6    403   1633 ( 80.44)     0  0    0   0   0   0     0 (0.00)    0   44 (2.69)
45      3    406   1627 ( 80.15)     0  0    0   0   0   0     0 (0.00)    0   44 (2.70)
44    150    556   1624 ( 80.00)     0  0    0   0   0   0     0 (0.00)    0   44 (2.71)
43     72    628   1474 ( 72.61)     0  0    0   0   0   0     0 (0.00)    0   44 (2.99)
42    276    904   1402 ( 69.06)     0  0    0   0   0   0     0 (0.00)    0   44 (3.14)
41     17    921   1126 ( 55.47)     0  0    0   0   0   0     0 (0.00)    0   44 (3.91)
40     80   1001   1109 ( 54.63)     0  0    0   0   0   0     0 (0.00)    0   44 (3.97)
38      8   1009   1029 ( 50.69)     0  0    0   0   0   0     0 (0.00)    0   44 (4.28)
37     64   1073   1021 ( 50.30)     0  0    0   0   0   0     0 (0.00)    0   44 (4.31)
36      6   1079    957 ( 47.14)     0  0    0   0   0   0     0 (0.00)    0   44 (4.60)
35     52   1131    951 ( 46.85)     0  0    0   0   0   0     0 (0.00)    0   44 (4.63)
34     21   1152    899 ( 44.29)     0  0    0   0   0   0     0 (0.00)    0   44 (4.89)
33     26   1178    878 ( 43.25)     0  0    0   0   0   0     0 (0.00)    0   44 (5.01)
32     17   1195    852 ( 41.97)     0  0    0   0   0   0     0 (0.00)    0   44 (5.16)
31     20   1215    835 ( 41.13)     0  0    0   0   0   0     0 (0.00)    0   44 (5.27)
30     16   1231    815 ( 40.15)     0  0    0   0   0   0     0 (0.00)    0   44 (5.40)
29     36   1267    799 ( 39.36)     0  0    0   0   0   0     0 (0.00)    0   44 (5.51)
28     25   1292    763 ( 37.59)     0  0    0   0   0   0     0 (0.00)    0   44 (5.77)
27     20   1312    738 ( 36.35)     0  0    0   0   0   0     0 (0.00)    0   44 (5.96)
26      7   1319    718 ( 35.37)     0  0    0   0   0   0     0 (0.00)    0   44 (6.13)
25     16   1335    711 ( 35.02)     0  0    0   0   0   0     0 (0.00)    0   44 (6.19)
24     19   1354    695 ( 34.24)     0  0    0   0   0   0     0 (0.00)    0   44 (6.33)
23     12   1366    676 ( 33.30)     0  0    0   0   0   0     0 (0.00)    0   44 (6.51)
22      8   1374    664 ( 32.71)     0  0    0   0   0   0     0 (0.00)    0   44 (6.63)
21     14   1388    656 ( 32.32)     0  0    0   0   0   0     0 (0.00)    0   44 (6.71)
20     13   1401    642 ( 31.63)     0  0    0   0   0   0     0 (0.00)    0   44 (6.85)
19     17   1418    629 ( 30.99)     0  0    0   0   0   0     0 (0.00)    0   44 (7.00)
18     11   1429    612 ( 30.15)     0  0    0   0   0   0     0 (0.00)    0   44 (7.19)
17     19   1448    601 ( 29.61)     0  0    0   0   0   0     0 (0.00)    0   44 (7.32)
16      8   1456    582 ( 28.67)     0  0    0   0   0   0     0 (0.00)    0   44 (7.56)
15     19   1475    574 ( 28.28)     0  0    0   0   0   0     0 (0.00)    0   44 (7.67)
14     19   1494    555 ( 27.34)     0  0    0   0   0   0     0 (0.00)    0   44 (7.93)
13     46   1540    536 ( 26.40)     0  0    0   0   0   0     0 (0.00)    0   44 (8.21)
12     33   1573    490 ( 24.14)     0  0    0   0   0   0     0 (0.00)    0   44 (8.98)
11     58   1631    457 ( 22.51)     0  0    0   6   0   0     6 (10.34)    6   44 (9.63)
10     56   1687    399 ( 19.66)     0  0    0   1   0   1     2 (3.57)    8   38 (9.52)
 9    136   1823    343 ( 16.90)     0  0    0   9   1   5    15 (11.03)   23   36 (10.50)
 8     84   1907    207 ( 10.20)     0  0    0   4   0   1     5 (5.95)   28   21 (10.14)
 7     79   1986    123 (  6.06)     0  0    0   4   1   1     6 (7.59)   34   16 (13.01)
 6     41   2027     44 (  2.17)     0  0    0   7   0   2     9 (21.95)   43   10 (22.73)
 4      3   2030      3 (  0.15)     0  0    0   1   0   0     1 (33.33)   44    1 (33.33)
-1     39   2069      0 (  0.00)    16  0    0   0   1   0     1 (2.56)   45    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
66    242    242   1741 (100.00)     0  0    0   0   0   0     0 (0.00)    0   11 (0.63)
61     14    256   1499 ( 86.10)     0  0    0   0   0   0     0 (0.00)    0   11 (0.73)
60    248    504   1485 ( 85.30)     0  0    0   0   0   0     0 (0.00)    0   11 (0.74)
58      2    506   1237 ( 71.05)     0  0    0   0   0   0     0 (0.00)    0   11 (0.89)
57     22    528   1235 ( 70.94)     0  0    0   0   0   0     0 (0.00)    0   11 (0.89)
56      8    536   1213 ( 69.67)     0  0    0   0   0   0     0 (0.00)    0   11 (0.91)
55      4    540   1205 ( 69.21)     0  0    0   0   0   0     0 (0.00)    0   11 (0.91)
54    156    696   1201 ( 68.98)     0  0    0   0   0   0     0 (0.00)    0   11 (0.92)
53     70    766   1045 ( 60.02)     0  0    0   0   0   0     0 (0.00)    0   11 (1.05)
52    247   1013    975 ( 56.00)     0  0    0   0   0   0     0 (0.00)    0   11 (1.13)
51     14   1027    728 ( 41.82)     0  0    0   0   0   0     0 (0.00)    0   11 (1.51)
50     69   1096    714 ( 41.01)     0  0    0   0   0   0     0 (0.00)    0   11 (1.54)
48      6   1102    645 ( 37.05)     0  0    0   0   0   0     0 (0.00)    0   11 (1.71)
47     59   1161    639 ( 36.70)     0  0    0   0   0   0     0 (0.00)    0   11 (1.72)
46      6   1167    580 ( 33.31)     0  0    0   0   0   0     0 (0.00)    0   11 (1.90)
45     42   1209    574 ( 32.97)     0  0    0   0   0   0     0 (0.00)    0   11 (1.92)
44     17   1226    532 ( 30.56)     0  0    0   0   0   0     0 (0.00)    0   11 (2.07)
43     20   1246    515 ( 29.58)     0  0    0   0   0   0     0 (0.00)    0   11 (2.14)
42     13   1259    495 ( 28.43)     0  0    0   0   0   0     0 (0.00)    0   11 (2.22)
41     13   1272    482 ( 27.69)     0  0    0   0   0   0     0 (0.00)    0   11 (2.28)
40     15   1287    469 ( 26.94)     0  0    0   0   0   0     0 (0.00)    0   11 (2.35)
39     24   1311    454 ( 26.08)     0  0    0   0   0   0     0 (0.00)    0   11 (2.42)
38     18   1329    430 ( 24.70)     0  0    0   0   0   0     0 (0.00)    0   11 (2.56)
37     15   1344    412 ( 23.66)     0  0    0   0   0   0     0 (0.00)    0   11 (2.67)
36      2   1346    397 ( 22.80)     0  0    0   0   0   0     0 (0.00)    0   11 (2.77)
35      9   1355    395 ( 22.69)     0  0    0   0   0   0     0 (0.00)    0   11 (2.78)
34     12   1367    386 ( 22.17)     0  0    0   0   0   0     0 (0.00)    0   11 (2.85)
33      7   1374    374 ( 21.48)     0  0    0   0   0   0     0 (0.00)    0   11 (2.94)
32     10   1384    367 ( 21.08)     0  0    0   0   0   0     0 (0.00)    0   11 (3.00)
31      8   1392    357 ( 20.51)     0  0    0   0   0   0     0 (0.00)    0   11 (3.08)
30      3   1395    349 ( 20.05)     0  0    0   0   0   0     0 (0.00)    0   11 (3.15)
29     10   1405    346 ( 19.87)     0  0    0   0   0   0     0 (0.00)    0   11 (3.18)
28     10   1415    336 ( 19.30)     0  0    0   0   0   0     0 (0.00)    0   11 (3.27)
27     11   1426    326 ( 18.72)     0  0    0   0   0   0     0 (0.00)    0   11 (3.37)
26      2   1428    315 ( 18.09)     0  0    0   0   0   0     0 (0.00)    0   11 (3.49)
25      7   1435    313 ( 17.98)     0  0    0   0   0   0     0 (0.00)    0   11 (3.51)
24      3   1438    306 ( 17.58)     0  0    0   0   0   0     0 (0.00)    0   11 (3.59)
23      2   1440    303 ( 17.40)     0  0    0   0   0   0     0 (0.00)    0   11 (3.63)
22      3   1443    301 ( 17.29)     0  0    0   0   0   0     0 (0.00)    0   11 (3.65)
21      8   1451    298 ( 17.12)     0  0    0   0   0   0     0 (0.00)    0   11 (3.69)
20     11   1462    290 ( 16.66)     0  0    0   0   0   0     0 (0.00)    0   11 (3.79)
19      9   1471    279 ( 16.03)     0  0    0   0   0   0     0 (0.00)    0   11 (3.94)
18      5   1476    270 ( 15.51)     0  0    0   0   0   0     0 (0.00)    0   11 (4.07)
17      8   1484    265 ( 15.22)     0  0    0   0   0   0     0 (0.00)    0   11 (4.15)
16      3   1487    257 ( 14.76)     0  0    0   0   0   0     0 (0.00)    0   11 (4.28)
15     23   1510    254 ( 14.59)     0  0    0   0   0   0     0 (0.00)    0   11 (4.33)
14      9   1519    231 ( 13.27)     0  0    0   0   0   0     0 (0.00)    0   11 (4.76)
13     28   1547    222 ( 12.75)     0  0    0   0   0   0     0 (0.00)    0   11 (4.95)
12     22   1569    194 ( 11.14)     0  0    0   0   0   0     0 (0.00)    0   11 (5.67)
11     29   1598    172 (  9.88)     0  0    0   1   0   0     1 (3.45)    1   11 (6.40)
10     17   1615    143 (  8.21)     0  0    0   0   0   0     0 (0.00)    1   10 (6.99)
 9     45   1660    126 (  7.24)     0  0    0   1   0   1     2 (4.44)    3   10 (7.94)
 8     35   1695     81 (  4.65)     0  0    0   1   0   0     1 (2.86)    4    8 (9.88)
 7     30   1725     46 (  2.64)     0  0    0   2   0   0     2 (6.67)    6    7 (15.22)
 6     13   1738     16 (  0.92)     0  0    0   4   0   0     4 (30.77)   10    5 (31.25)
 4      3   1741      3 (  0.17)     0  0    0   1   0   0     1 (33.33)   11    1 (33.33)
-1    328   2069      0 (  0.00)    16  0    0  22   3   9    34 (10.37)   45    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     182      182        2
  7       6      188        5
  8      12      200       14
  9      18      218       15
 10      11      229       18
 11       8      237       19
 12      13      250       21
 13      20      270       18
 14       8      278       16
 15      16      294       20
 16       3      297       17
 17       7      304       14
 18       1      305       14
 19       5      310       16
 20       8      318       13
 21       3      321       10
 23       1      322        9
 24       2      324        9
 25       2      326        9
 26       1      327       10
 27       5      332       10
 28       8      340       13
 29       7      347       13
 30       2      349       12
 31       6      355       10
 32       7      362       10
 33       3      365       10
 34       4      369       10
 35       7      376       10
 36       1      377        9
 37       9      386        8
 38       9      395       10
 39      12      407       13
 40       7      414       14
 41       7      421       13
 42       6      427       14
 43      10      437       15
 44      10      447       18
 45      21      468       24
 46       3      471       26
 47      30      501       27
 48       3      504       28
 50      35      539       22
 51       7      546       24
 52     124      670       37
 53      35      705       40
 54      78      783       48
 55       2      785       46
 56       4      789       44
 57      11      800       47
 58       1      801       46
 60     124      925       35
 61       7      932       33
 66     121     1053        1

SS region: 1053 (100.00%), flagged: 2 (0.19%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality):
   915  D     ce040109f1      (0)/(0)  913 CAGG / CAG
   920  S     ce040109f1      (0)/(0)  919 TCC / TAC
   911  I     de040109f1      (0)/(0)  911 TA / TTA
   926  S     de040109f1      (0)/(0)  925 GTG / GCG
   939  S     de040109f1      (0)/(0)  931 CCAATGCTTC / CGATTCTGC
   952  S     de040109f1      (0)/(0)  951 AGT / AAT
   957  I     de040109f1      (0)/(0)  956 ATT / AACT
   966  D     de040109f1      (0)/(0)  961 AACGCGC / ACCCCC
   977  D     de040109f1      (0)/(0)  973 CTTCTA / CGTCA
   981  S     de040109f1      (0)/(0)  980 AAG / AGG
   993  D     de040109f1      (0)/(0)  991 TTAA / TCA
  1004  S     de040109f1      (0)/(0)  1001 ATTAA / AATTA
  1019  D     de040109f1      (0)/(0)  1011 CGCCGCCCTC / CTTCCCACC
  1027  S     de040109f1      (0)/(0)  1026 GTA / GAA
  1035  D     de040109f1      (0)/(0)  1030 TTTGCTC / TTGCC
  1047  S     de040109f1      (0)/(0)  1043 ACTTTG / AGTTGG

0 HQ discrepancies in 0 reads.
16 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 4.  2 reads; 1057 bp (untrimmed), 888 (trimmed).  Isolated contig.
      1  1057 ce040109r1   1016 (  0)  0.38 0.38 0.19    0 ( 19)    0 (149) 
      3  1057 de040109r1    869 (  0)  2.30 0.10 1.82    8 ( 18)    5 (135) 

Overall discrep rates (%):             1.33 0.24 1.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 66     232  21.9     232  21.9    0.00
 61      48   4.5     280  26.5    0.00
 60      58   5.5     338  32.0    0.00
 58       2   0.2     340  32.2    0.00
 57       8   0.8     348  32.9    0.00
 56       6   0.6     354  33.5    0.00
 55       6   0.6     360  34.1    0.00
 54      54   5.1     414  39.2    0.00
 53      35   3.3     449  42.5    0.00
 52      66   6.2     515  48.7    0.00
 51       3   0.3     518  49.0    0.00
 50      45   4.3     563  53.3    0.00
 49       2   0.2     565  53.5    0.00
 48       2   0.2     567  53.6    0.00
 47      15   1.4     582  55.1    0.00
 46       1   0.1     583  55.2    0.00
 45      17   1.6     600  56.8    0.00
 44       6   0.6     606  57.3    0.00
 43       8   0.8     614  58.1    0.00
 42       6   0.6     620  58.7    0.00
 41       2   0.2     622  58.8    0.00
 40       3   0.3     625  59.1    0.00
 39      29   2.7     654  61.9    0.01
 38       7   0.7     661  62.5    0.01
 37       6   0.6     667  63.1    0.01
 36       3   0.3     670  63.4    0.01
 35      13   1.2     683  64.6    0.01
 34       3   0.3     686  64.9    0.02
 33       5   0.5     691  65.4    0.02
 32       6   0.6     697  65.9    0.02
 31       2   0.2     699  66.1    0.02
 30       1   0.1     700  66.2    0.02
 29       4   0.4     704  66.6    0.03
 27       5   0.5     709  67.1    0.04
 26       2   0.2     711  67.3    0.04
 25       8   0.8     719  68.0    0.07
 24       3   0.3     722  68.3    0.08
 23       2   0.2     724  68.5    0.09
 22       4   0.4     728  68.9    0.12
 21       6   0.6     734  69.4    0.16
 20       7   0.7     741  70.1    0.23
 19      12   1.1     753  71.2    0.39
 18       8   0.8     761  72.0    0.51
 17       5   0.5     766  72.5    0.61
 16      15   1.4     781  73.9    0.99
 15      22   2.1     803  76.0    1.69
 14       7   0.7     810  76.6    1.96
 13      11   1.0     821  77.7    2.52
 12      10   0.9     831  78.6    3.15
 11      12   1.1     843  79.8    4.10
 10       9   0.9     852  80.6    5.00
  9      21   2.0     873  82.6    7.64
  8       8   0.8     881  83.3    8.91
  7       5   0.5     886  83.8    9.91
  6       2   0.2     888  84.0   10.41
 -1     169  16.0    1057 100.0  179.41   (quality -1 = terminal quality 0)

Avg. full length: 1057.0, trimmed (qual > -1): 888.0
Avg. quality: 39.7 per base

Initial, terminal qual 0 segments:  1-20, 909-1057

Regions of LLR- adjusted quality < 2.0:
1-29, 31-42, 45-48, 82-85, 720-721, 747-751, 768-775, 782-789, 
793-805, 814-819, 822-832, 836-849, 854-856, 860-907, 909-1057, 

15 regions, avg size 21.1, avg spacing 70.5

First_start: 20, last_end: 922

Slack, # used pairs (max_score), unused
 0     0  ( 0.0)     0 ( 0.0)        1
 1     1  (21.1)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 1058 - right        0+      de040109r1   (   3)    No           1054+

Bottom strand: 
 left - right     1057+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56    266    266   2068 (100.00)     0  0    0   0   0   0     0 (0.00)    0   52 (2.51)
51     59    325   1802 ( 87.14)     0  0    0   0   0   0     0 (0.00)    0   52 (2.89)
50    129    454   1743 ( 84.28)     0  0    0   0   0   0     0 (0.00)    0   52 (2.98)
48      3    457   1614 ( 78.05)     0  0    0   0   0   0     0 (0.00)    0   52 (3.22)
47     21    478   1611 ( 77.90)     0  0    0   0   0   0     0 (0.00)    0   52 (3.23)
46     18    496   1590 ( 76.89)     0  0    0   0   0   0     0 (0.00)    0   52 (3.27)
45     10    506   1572 ( 76.02)     0  0    0   0   0   0     0 (0.00)    0   52 (3.31)
44    115    621   1562 ( 75.53)     0  0    0   0   0   0     0 (0.00)    0   52 (3.33)
43     59    680   1447 ( 69.97)     0  0    0   0   0   0     0 (0.00)    0   52 (3.59)
42    201    881   1388 ( 67.12)     0  0    0   0   0   0     0 (0.00)    0   52 (3.75)
41     13    894   1187 ( 57.40)     0  0    0   0   0   0     0 (0.00)    0   52 (4.38)
40     96    990   1174 ( 56.77)     0  0    0   0   0   0     0 (0.00)    0   52 (4.43)
39      6    996   1078 ( 52.13)     0  0    0   0   0   0     0 (0.00)    0   52 (4.82)
38      7   1003   1072 ( 51.84)     0  0    0   0   0   0     0 (0.00)    0   52 (4.85)
37     55   1058   1065 ( 51.50)     0  0    0   0   0   0     0 (0.00)    0   52 (4.88)
36      4   1062   1010 ( 48.84)     0  0    0   0   0   0     0 (0.00)    0   52 (5.15)
35     46   1108   1006 ( 48.65)     0  0    0   0   0   0     0 (0.00)    0   52 (5.17)
34     12   1120    960 ( 46.42)     0  0    0   0   0   0     0 (0.00)    0   52 (5.42)
33     32   1152    948 ( 45.84)     0  0    0   0   0   0     0 (0.00)    0   52 (5.49)
32     12   1164    916 ( 44.29)     0  0    0   0   0   0     0 (0.00)    0   52 (5.68)
31      4   1168    904 ( 43.71)     0  0    0   0   0   0     0 (0.00)    0   52 (5.75)
30     12   1180    900 ( 43.52)     0  0    0   0   0   0     0 (0.00)    0   52 (5.78)
29     56   1236    888 ( 42.94)     0  0    0   0   0   0     0 (0.00)    0   52 (5.86)
28     14   1250    832 ( 40.23)     0  0    0   0   0   0     0 (0.00)    0   52 (6.25)
27     16   1266    818 ( 39.56)     0  0    0   0   0   0     0 (0.00)    0   52 (6.36)
26     10   1276    802 ( 38.78)     0  0    0   0   0   0     0 (0.00)    0   52 (6.48)
25     31   1307    792 ( 38.30)     0  0    0   0   0   0     0 (0.00)    0   52 (6.57)
24     27   1334    761 ( 36.80)     0  0    0   0   0   0     0 (0.00)    0   52 (6.83)
23     12   1346    734 ( 35.49)     0  0    0   0   0   0     0 (0.00)    0   52 (7.08)
22     16   1362    722 ( 34.91)     0  0    0   0   0   0     0 (0.00)    0   52 (7.20)
21     16   1378    706 ( 34.14)     0  0    0   0   0   0     0 (0.00)    0   52 (7.37)
20     15   1393    690 ( 33.37)     0  0    0   0   0   0     0 (0.00)    0   52 (7.54)
19     25   1418    675 ( 32.64)     0  0    0   0   0   0     0 (0.00)    0   52 (7.70)
18     16   1434    650 ( 31.43)     0  0    0   0   0   0     0 (0.00)    0   52 (8.00)
17     14   1448    634 ( 30.66)     0  0    0   0   0   0     0 (0.00)    0   52 (8.20)
16     31   1479    620 ( 29.98)     0  0    0   0   0   0     0 (0.00)    0   52 (8.39)
15     30   1509    589 ( 28.48)     0  0    0   0   0   2     2 (6.67)    2   52 (8.83)
14     21   1530    559 ( 27.03)     0  0    0   0   0   0     0 (0.00)    2   50 (8.94)
13     34   1564    538 ( 26.02)     0  0    0   1   1   1     3 (8.82)    5   50 (9.29)
12     42   1606    504 ( 24.37)     0  0    0   1   1   1     3 (7.14)    8   47 (9.33)
11     45   1651    462 ( 22.34)     0  0    0   0   0   0     0 (0.00)    8   44 (9.52)
10     72   1723    417 ( 20.16)     0  0    0   0   0   4     4 (5.56)   12   44 (10.55)
 9    149   1872    345 ( 16.68)     0  0    0   9   0   4    13 (8.72)   25   40 (11.59)
 8     63   1935    196 (  9.48)     0  0    0   5   1   2     8 (12.70)   33   27 (13.78)
 7     84   2019    133 (  6.43)     0  0    0   4   1   4     9 (10.71)   42   19 (14.29)
 6     46   2065     49 (  2.37)     0  0    0   7   1   1     9 (19.57)   51   10 (20.41)
 4      3   2068      3 (  0.15)     0  0    0   1   0   0     1 (33.33)   52    1 (33.33)
-1     15   2083      0 (  0.00)    13  0    0   0   0   0     0 (0.00)   52    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
66    458    458   1775 (100.00)     0  0    0   0   0   0     0 (0.00)    0   18 (1.01)
61     96    554   1317 ( 74.20)     0  0    0   0   0   0     0 (0.00)    0   18 (1.37)
60    116    670   1221 ( 68.79)     0  0    0   0   0   0     0 (0.00)    0   18 (1.47)
58      4    674   1105 ( 62.25)     0  0    0   0   0   0     0 (0.00)    0   18 (1.63)
57     16    690   1101 ( 62.03)     0  0    0   0   0   0     0 (0.00)    0   18 (1.63)
56     18    708   1085 ( 61.13)     0  0    0   0   0   0     0 (0.00)    0   18 (1.66)
55     12    720   1067 ( 60.11)     0  0    0   0   0   0     0 (0.00)    0   18 (1.69)
54    108    828   1055 ( 59.44)     0  0    0   0   0   0     0 (0.00)    0   18 (1.71)
53     70    898    947 ( 53.35)     0  0    0   0   0   0     0 (0.00)    0   18 (1.90)
52    132   1030    877 ( 49.41)     0  0    0   0   0   0     0 (0.00)    0   18 (2.05)
51      6   1036    745 ( 41.97)     0  0    0   0   0   0     0 (0.00)    0   18 (2.42)
50     86   1122    739 ( 41.63)     0  0    0   0   0   0     0 (0.00)    0   18 (2.44)
49      4   1126    653 ( 36.79)     0  0    0   0   0   0     0 (0.00)    0   18 (2.76)
48      4   1130    649 ( 36.56)     0  0    0   0   0   0     0 (0.00)    0   18 (2.77)
47     30   1160    645 ( 36.34)     0  0    0   0   0   0     0 (0.00)    0   18 (2.79)
46      1   1161    615 ( 34.65)     0  0    0   0   0   0     0 (0.00)    0   18 (2.93)
45     34   1195    614 ( 34.59)     0  0    0   0   0   0     0 (0.00)    0   18 (2.93)
44     10   1205    580 ( 32.68)     0  0    0   0   0   0     0 (0.00)    0   18 (3.10)
43     13   1218    570 ( 32.11)     0  0    0   0   0   0     0 (0.00)    0   18 (3.16)
42     12   1230    557 ( 31.38)     0  0    0   0   0   0     0 (0.00)    0   18 (3.23)
41      4   1234    545 ( 30.70)     0  0    0   0   0   0     0 (0.00)    0   18 (3.30)
40      7   1241    541 ( 30.48)     0  0    0   0   0   0     0 (0.00)    0   18 (3.33)
39     52   1293    534 ( 30.08)     0  0    0   0   0   0     0 (0.00)    0   18 (3.37)
38     14   1307    482 ( 27.15)     0  0    0   0   0   0     0 (0.00)    0   18 (3.73)
37      9   1316    468 ( 26.37)     0  0    0   0   0   0     0 (0.00)    0   18 (3.85)
36      6   1322    459 ( 25.86)     0  0    0   0   0   0     0 (0.00)    0   18 (3.92)
35     20   1342    453 ( 25.52)     0  0    0   0   0   0     0 (0.00)    0   18 (3.97)
34      4   1346    433 ( 24.39)     0  0    0   0   0   0     0 (0.00)    0   18 (4.16)
33      9   1355    429 ( 24.17)     0  0    0   0   0   0     0 (0.00)    0   18 (4.20)
32     10   1365    420 ( 23.66)     0  0    0   0   0   0     0 (0.00)    0   18 (4.29)
31      3   1368    410 ( 23.10)     0  0    0   0   0   0     0 (0.00)    0   18 (4.39)
30      4   1372    407 ( 22.93)     0  0    0   0   0   0     0 (0.00)    0   18 (4.42)
29     10   1382    403 ( 22.70)     0  0    0   0   0   0     0 (0.00)    0   18 (4.47)
28      1   1383    393 ( 22.14)     0  0    0   0   0   0     0 (0.00)    0   18 (4.58)
27      6   1389    392 ( 22.08)     0  0    0   0   0   0     0 (0.00)    0   18 (4.59)
26      5   1394    386 ( 21.75)     0  0    0   0   0   0     0 (0.00)    0   18 (4.66)
25     19   1413    381 ( 21.46)     0  0    0   0   0   0     0 (0.00)    0   18 (4.72)
24      8   1421    362 ( 20.39)     0  0    0   0   0   0     0 (0.00)    0   18 (4.97)
23      2   1423    354 ( 19.94)     0  0    0   0   0   0     0 (0.00)    0   18 (5.08)
22      6   1429    352 ( 19.83)     0  0    0   0   0   0     0 (0.00)    0   18 (5.11)
21     10   1439    346 ( 19.49)     0  0    0   0   0   0     0 (0.00)    0   18 (5.20)
20     10   1449    336 ( 18.93)     0  0    0   0   0   0     0 (0.00)    0   18 (5.36)
19     16   1465    326 ( 18.37)     0  0    0   0   0   0     0 (0.00)    0   18 (5.52)
18     10   1475    310 ( 17.46)     0  0    0   0   0   0     0 (0.00)    0   18 (5.81)
17      8   1483    300 ( 16.90)     0  0    0   0   0   0     0 (0.00)    0   18 (6.00)
16     20   1503    292 ( 16.45)     0  0    0   0   0   0     0 (0.00)    0   18 (6.16)
15     36   1539    272 ( 15.32)     0  0    0   0   0   2     2 (5.56)    2   18 (6.62)
14     14   1553    236 ( 13.30)     0  0    0   0   0   0     0 (0.00)    2   16 (6.78)
13     18   1571    222 ( 12.51)     0  0    0   0   1   0     1 (5.56)    3   16 (7.21)
12     26   1597    204 ( 11.49)     0  0    0   0   1   0     1 (3.85)    4   15 (7.35)
11     24   1621    178 ( 10.03)     0  0    0   0   0   0     0 (0.00)    4   14 (7.87)
10     28   1649    154 (  8.68)     0  0    0   0   0   1     1 (3.57)    5   14 (9.09)
 9     53   1702    126 (  7.10)     0  0    0   1   0   2     3 (5.66)    8   13 (10.32)
 8     26   1728     73 (  4.11)     0  0    0   1   1   0     2 (7.69)   10   10 (13.70)
 7     34   1762     47 (  2.65)     0  0    0   2   1   0     3 (8.82)   13    8 (17.02)
 6     13   1775     13 (  0.73)     0  0    0   5   0   0     5 (38.46)   18    5 (38.46)
-1    308   2083      0 (  0.00)    13  0    0  19   1  14    34 (11.04)   52    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     169      169        2
  6       2      171        3
  7       5      176        6
  8       8      184       10
  9      21      205       14
 10       9      214       18
 11      12      226       19
 12      10      236       20
 13      11      247       20
 14       7      254       21
 15      22      276       23
 16      15      291       21
 17       5      296       20
 18       8      304       20
 19      12      316       15
 20       7      323       14
 21       6      329       13
 22       4      333       12
 23       2      335       12
 24       3      338       13
 25       8      346       12
 26       2      348       11
 27       5      353        8
 29       4      357        8
 30       1      358        9
 31       2      360        9
 32       6      366        9
 33       5      371        9
 34       3      374       10
 35      13      387       12
 36       3      390       12
 37       6      396       12
 38       7      403       13
 39      29      432       16
 40       3      435       15
 41       2      437       14
 42       6      443       13
 43       8      451       11
 44       6      457        9
 45      17      474       10
 46       1      475       11
 47      15      490       13
 48       2      492       13
 49       2      494       13
 50      45      539       19
 51       3      542       20
 52      66      608       33
 53      35      643       36
 54      54      697       50
 55       6      703       50
 56       6      709       49
 57       8      717       49
 58       2      719       48
 60      58      777       45
 61      48      825       40
 66     232     1057        1

SS region: 1057 (100.00%), flagged: 4 (0.38%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality):
*   20  D     ce040109r1      (7)/(6)  18 GGGT / GGT
*   40  D     ce040109r1      (33)/(28)  38 CTTA / CTA
    15  S     de040109r1      (0)/(0)  14 CTT / CGT
   924  S     de040109r1      (0)/(0)  913 TTCCGCCAACCTT / TCACGCAATCGT
   933  D     de040109r1      (0)/(0)  930 CTATT / CCTAT
   939  S     de040109r1      (0)/(0)  938 GTT / GCT
   952  S     de040109r1      (0)/(0)  942 CCGAACTTCCCG / CGGAATCACAG
   958  D     de040109r1      (0)/(0)  956 GCTG / GCG
   968  S     de040109r1      (0)/(0)  963 ATTTAAC / ACTATC
   974  S     de040109r1      (0)/(0)  973 CTT / CGT
   982  D     de040109r1      (0)/(0)  980 TTTA / TAA
   987  D     de040109r1      (0)/(0)  985 TGGA / TGA
  1005  D     de040109r1      (0)/(0)  1001 AAATGA / AGAA
  1014  D     de040109r1      (0)/(0)  1008 CGAATTCT / CGATTT
  1026  D     de040109r1      (0)/(0)  1020 TTTCCAGC / TTCCAC
  1033  S     de040109r1      (0)/(0)  1032 GGA / GAA
  1045  D     de040109r1      (0)/(0)  1037 AAACAACTCC / ACCCCACTC

0 HQ discrepancies in 0 reads.
17 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 5.  2 reads; 1051 bp (untrimmed), 616 (trimmed).  Isolated contig.
    -51  1084 cg060109r1    649 (  0)  3.59 0.53 0.13   52 ( 52)  331 (471) 
    -44  1051 be070109r1    991 (  0)  0.38 0.00 0.00   45 ( 45)    0 (435) 

Overall discrep rates (%):             1.72 0.22 0.06

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 66       2   0.2       2   0.2    0.00
 60      23   2.2      25   2.4    0.00
 58       3   0.3      28   2.7    0.00
 57       5   0.5      33   3.1    0.00
 56       3   0.3      36   3.4    0.00
 54      61   5.8      97   9.2    0.00
 53       1   0.1      98   9.3    0.00
 52      86   8.2     184  17.5    0.00
 51       1   0.1     185  17.6    0.00
 50      18   1.7     203  19.3    0.00
 49      14   1.3     217  20.6    0.00
 48       6   0.6     223  21.2    0.00
 47      45   4.3     268  25.5    0.00
 46       4   0.4     272  25.9    0.00
 45      41   3.9     313  29.8    0.00
 44      15   1.4     328  31.2    0.00
 43      28   2.7     356  33.9    0.01
 42       4   0.4     360  34.3    0.01
 41      11   1.0     371  35.3    0.01
 40      19   1.8     390  37.1    0.01
 39      13   1.2     403  38.3    0.01
 38      13   1.2     416  39.6    0.01
 37      10   1.0     426  40.5    0.01
 36       4   0.4     430  40.9    0.02
 35      10   1.0     440  41.9    0.02
 34       8   0.8     448  42.6    0.02
 33       7   0.7     455  43.3    0.03
 32       6   0.6     461  43.9    0.03
 31      11   1.0     472  44.9    0.04
 30       3   0.3     475  45.2    0.04
 29      11   1.0     486  46.2    0.05
 28       6   0.6     492  46.8    0.06
 27       8   0.8     500  47.6    0.08
 26       5   0.5     505  48.0    0.09
 25      11   1.0     516  49.1    0.13
 22       1   0.1     517  49.2    0.13
 21       2   0.2     519  49.4    0.15
 20       2   0.2     521  49.6    0.17
 19       4   0.4     525  50.0    0.22
 18       1   0.1     526  50.0    0.24
 17       3   0.3     529  50.3    0.30
 16       6   0.6     535  50.9    0.45
 15      35   3.3     570  54.2    1.55
 14       2   0.2     572  54.4    1.63
 13      11   1.0     583  55.5    2.18
 12       5   0.5     588  55.9    2.50
 11      11   1.0     599  57.0    3.37
 10      12   1.1     611  58.1    4.57
  9       3   0.3     614  58.4    4.95
  8       2   0.2     616  58.6    5.27
 -1     435  41.4    1051 100.0  440.27   (quality -1 = terminal quality 0)

Avg. full length: 1051.0, trimmed (qual > -1): 616.0
Avg. quality: 23.6 per base

Initial, terminal qual 0 segments:  (None), 617-1051

Regions of LLR- adjusted quality < 2.0:
31-35, 369-370, 400, 466-469, 498-502, 512-516, 526-528, 532-537, 
544-554, 560-577, 579-594, 597-615, 617-1051, 

13 regions, avg size 40.8, avg spacing 80.8

First_start: 1, last_end: 616

Slack, # used pairs (max_score), unused
 0     1  (15.8)     0 ( 0.0)        1

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 1052 - right        0+      be070109r1   ( -44)    No           1095+

Bottom strand: 
 left - right     1051+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56      5      5   1509 (100.00)     0  0    0   0   0   0     0 (0.00)    0   36 (2.39)
50     24     29   1504 ( 99.67)     0  0    0   0   0   0     0 (0.00)    0   36 (2.39)
48      6     35   1480 ( 98.08)     0  0    0   0   0   0     0 (0.00)    0   36 (2.43)
47      5     40   1474 ( 97.68)     0  0    0   0   0   0     0 (0.00)    0   36 (2.44)
46      1     41   1469 ( 97.35)     0  0    0   0   0   0     0 (0.00)    0   36 (2.45)
44     64    105   1468 ( 97.28)     0  0    0   0   0   0     0 (0.00)    0   36 (2.45)
43      2    107   1404 ( 93.04)     0  0    0   0   0   0     0 (0.00)    0   36 (2.56)
42    106    213   1402 ( 92.91)     0  0    0   0   0   0     0 (0.00)    0   36 (2.57)
41      7    220   1296 ( 85.88)     0  0    0   0   0   0     0 (0.00)    0   36 (2.78)
40     34    254   1289 ( 85.42)     0  0    0   0   0   0     0 (0.00)    0   36 (2.79)
39     20    274   1255 ( 83.17)     0  0    0   0   0   0     0 (0.00)    0   36 (2.87)
38      8    282   1235 ( 81.84)     0  0    0   0   0   0     0 (0.00)    0   36 (2.91)
37     91    373   1227 ( 81.31)     0  0    0   0   0   0     0 (0.00)    0   36 (2.93)
36      5    378   1136 ( 75.28)     0  0    0   0   0   0     0 (0.00)    0   36 (3.17)
35     74    452   1131 ( 74.95)     0  0    0   0   0   0     0 (0.00)    0   36 (3.18)
34     25    477   1057 ( 70.05)     0  0    0   0   0   0     0 (0.00)    0   36 (3.41)
33     60    537   1032 ( 68.39)     0  0    0   0   0   0     0 (0.00)    0   36 (3.49)
32     17    554    972 ( 64.41)     0  0    0   0   0   0     0 (0.00)    0   36 (3.70)
31     25    579    955 ( 63.29)     0  0    0   0   0   0     0 (0.00)    0   36 (3.77)
30     47    626    930 ( 61.63)     0  0    0   0   0   0     0 (0.00)    0   36 (3.87)
29     45    671    883 ( 58.52)     0  0    0   0   0   0     0 (0.00)    0   36 (4.08)
28     27    698    838 ( 55.53)     0  0    0   0   0   0     0 (0.00)    0   36 (4.30)
27     23    721    811 ( 53.74)     0  0    0   0   0   0     0 (0.00)    0   36 (4.44)
26     16    737    788 ( 52.22)     0  0    0   0   0   0     0 (0.00)    0   36 (4.57)
25     20    757    772 ( 51.16)     0  0    0   0   0   0     0 (0.00)    0   36 (4.66)
24     16    773    752 ( 49.83)     0  0    0   0   0   0     0 (0.00)    0   36 (4.79)
23     13    786    736 ( 48.77)     0  0    0   0   0   0     0 (0.00)    0   36 (4.89)
22     27    813    723 ( 47.91)     0  0    0   0   0   0     0 (0.00)    0   36 (4.98)
21     39    852    696 ( 46.12)     0  0    0   0   0   0     0 (0.00)    0   36 (5.17)
20     18    870    657 ( 43.54)     0  0    0   0   0   0     0 (0.00)    0   36 (5.48)
19     34    904    639 ( 42.35)     0  0    0   0   0   0     0 (0.00)    0   36 (5.63)
18     18    922    605 ( 40.09)     0  0    0   0   0   0     0 (0.00)    0   36 (5.95)
17     21    943    587 ( 38.90)     0  0    0   0   0   0     0 (0.00)    0   36 (6.13)
16     25    968    566 ( 37.51)     0  0    0   0   0   0     0 (0.00)    0   36 (6.36)
15     44   1012    541 ( 35.85)     0  0    0   0   0   0     0 (0.00)    0   36 (6.65)
14     32   1044    497 ( 32.94)     0  0    0   1   1   0     2 (6.25)    2   36 (7.24)
13     59   1103    465 ( 30.82)     0  0    0   2   0   0     2 (3.39)    4   34 (7.31)
12     43   1146    406 ( 26.91)     0  0    0   1   0   0     1 (2.33)    5   32 (7.88)
11     89   1235    363 ( 24.06)     0  0    0   6   0   0     6 (6.74)   11   31 (8.54)
10     92   1327    274 ( 18.16)     0  0    0  10   0   1    11 (11.96)   22   25 (9.12)
 9     95   1422    182 ( 12.06)     0  0    0   4   1   0     5 (5.26)   27   14 (7.69)
 8     50   1472     87 (  5.77)     0  0    0   4   0   0     4 (8.00)   31    9 (10.34)
 7     13   1485     37 (  2.45)     0  0    0   0   1   0     1 (7.69)   32    5 (13.51)
 6     24   1509     24 (  1.59)     0  0    0   3   1   0     4 (16.67)   36    4 (16.67)
-1    298   1807      0 (  0.00)   298  0    0   0   0   0     0 (0.00)   36    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
66      4      4   1232 (100.00)     0  0    0   0   0   0     0 (0.00)    0    8 (0.65)
60     46     50   1228 ( 99.68)     0  0    0   0   0   0     0 (0.00)    0    8 (0.65)
58      5     55   1182 ( 95.94)     0  0    0   0   0   0     0 (0.00)    0    8 (0.68)
57     10     65   1177 ( 95.54)     0  0    0   0   0   0     0 (0.00)    0    8 (0.68)
56      4     69   1167 ( 94.72)     0  0    0   0   0   0     0 (0.00)    0    8 (0.69)
54    121    190   1163 ( 94.40)     0  0    0   0   0   0     0 (0.00)    0    8 (0.69)
53      2    192   1042 ( 84.58)     0  0    0   0   0   0     0 (0.00)    0    8 (0.77)
52    169    361   1040 ( 84.42)     0  0    0   0   0   0     0 (0.00)    0    8 (0.77)
51      2    363    871 ( 70.70)     0  0    0   0   0   0     0 (0.00)    0    8 (0.92)
50     38    401    869 ( 70.54)     0  0    0   0   0   0     0 (0.00)    0    8 (0.92)
49     28    429    831 ( 67.45)     0  0    0   0   0   0     0 (0.00)    0    8 (0.96)
48     12    441    803 ( 65.18)     0  0    0   0   0   0     0 (0.00)    0    8 (1.00)
47     88    529    791 ( 64.20)     0  0    0   0   0   0     0 (0.00)    0    8 (1.01)
46      8    537    703 ( 57.06)     0  0    0   0   0   0     0 (0.00)    0    8 (1.14)
45     80    617    695 ( 56.41)     0  0    0   0   0   0     0 (0.00)    0    8 (1.15)
44     30    647    615 ( 49.92)     0  0    0   0   0   0     0 (0.00)    0    8 (1.30)
43     55    702    585 ( 47.48)     0  0    0   0   0   0     0 (0.00)    0    8 (1.37)
42     11    713    530 ( 43.02)     0  0    0   0   0   0     0 (0.00)    0    8 (1.51)
41     18    731    519 ( 42.13)     0  0    0   0   0   0     0 (0.00)    0    8 (1.54)
40     31    762    501 ( 40.67)     0  0    0   0   0   0     0 (0.00)    0    8 (1.60)
39     21    783    470 ( 38.15)     0  0    0   0   0   0     0 (0.00)    0    8 (1.70)
38     19    802    449 ( 36.44)     0  0    0   0   0   0     0 (0.00)    0    8 (1.78)
37     22    824    430 ( 34.90)     0  0    0   0   0   0     0 (0.00)    0    8 (1.86)
36      6    830    408 ( 33.12)     0  0    0   0   0   0     0 (0.00)    0    8 (1.96)
35     15    845    402 ( 32.63)     0  0    0   0   0   0     0 (0.00)    0    8 (1.99)
34     17    862    387 ( 31.41)     0  0    0   0   0   0     0 (0.00)    0    8 (2.07)
33     12    874    370 ( 30.03)     0  0    0   0   0   0     0 (0.00)    0    8 (2.16)
32      9    883    358 ( 29.06)     0  0    0   0   0   0     0 (0.00)    0    8 (2.23)
31     16    899    349 ( 28.33)     0  0    0   0   0   0     0 (0.00)    0    8 (2.29)
30     13    912    333 ( 27.03)     0  0    0   0   0   0     0 (0.00)    0    8 (2.40)
29     24    936    320 ( 25.97)     0  0    0   0   0   0     0 (0.00)    0    8 (2.50)
28     15    951    296 ( 24.03)     0  0    0   0   0   0     0 (0.00)    0    8 (2.70)
27     10    961    281 ( 22.81)     0  0    0   0   0   0     0 (0.00)    0    8 (2.85)
26      8    969    271 ( 22.00)     0  0    0   0   0   0     0 (0.00)    0    8 (2.95)
25     22    991    263 ( 21.35)     0  0    0   0   0   0     0 (0.00)    0    8 (3.04)
24      1    992    241 ( 19.56)     0  0    0   0   0   0     0 (0.00)    0    8 (3.32)
23      3    995    240 ( 19.48)     0  0    0   0   0   0     0 (0.00)    0    8 (3.33)
22      5   1000    237 ( 19.24)     0  0    0   0   0   0     0 (0.00)    0    8 (3.38)
21     10   1010    232 ( 18.83)     0  0    0   0   0   0     0 (0.00)    0    8 (3.45)
20      3   1013    222 ( 18.02)     0  0    0   0   0   0     0 (0.00)    0    8 (3.60)
19     11   1024    219 ( 17.78)     0  0    0   0   0   0     0 (0.00)    0    8 (3.65)
18      3   1027    208 ( 16.88)     0  0    0   0   0   0     0 (0.00)    0    8 (3.85)
17     12   1039    205 ( 16.64)     0  0    0   0   0   0     0 (0.00)    0    8 (3.90)
16     11   1050    193 ( 15.67)     0  0    0   0   0   0     0 (0.00)    0    8 (4.15)
15     62   1112    182 ( 14.77)     0  0    0   0   0   0     0 (0.00)    0    8 (4.40)
14      4   1116    120 (  9.74)     0  0    0   0   0   0     0 (0.00)    0    8 (6.67)
13     19   1135    116 (  9.42)     0  0    0   0   0   0     0 (0.00)    0    8 (6.90)
12     15   1150     97 (  7.87)     0  0    0   0   0   0     0 (0.00)    0    8 (8.25)
11     24   1174     82 (  6.66)     0  0    0   1   0   0     1 (4.17)    1    8 (9.76)
10     36   1210     58 (  4.71)     0  0    0   4   0   1     5 (13.89)    6    7 (12.07)
 9     10   1220     22 (  1.79)     0  0    0   1   0   0     1 (10.00)    7    2 (9.09)
 8     12   1232     12 (  0.97)     0  0    0   1   0   0     1 (8.33)    8    1 (8.33)
-1    575   1807      0 (  0.00)   298  0    0  24   4   0    28 (4.87)   36    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     435      435        1
  8       2      437        2
  9       3      440        3
 10      12      452        6
 11      11      463       10
 12       5      468       11
 13      11      479        7
 14       2      481        7
 15      35      516       18
 16       6      522       17
 17       3      525       16
 18       1      526       16
 19       4      530       13
 20       2      532       13
 21       2      534       11
 22       1      535       11
 25      11      546       13
 26       5      551       15
 27       8      559       15
 28       6      565       15
 29      11      576       18
 30       3      579       19
 31      11      590       20
 32       6      596       19
 33       7      603       21
 34       8      611       22
 35      10      621       22
 36       4      625       24
 37      10      635       22
 38      13      648       22
 39      13      661       25
 40      19      680       24
 41      11      691       21
 42       4      695       22
 43      28      723       23
 44      15      738       26
 45      41      779       32
 46       4      783       32
 47      45      828       39
 48       6      834       38
 49      14      848       40
 50      18      866       38
 51       1      867       38
 52      86      953       27
 53       1      954       27
 54      61     1015       16
 56       3     1018       16
 57       5     1023       13
 58       3     1026       12
 60      23     1049        2
 66       2     1051        1

SS region: 1051 (100.00%), flagged: 3 (0.29%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality):
   622  S     cg060109r1      (0)/(0)  621 GGT / GTT
   637  S     cg060109r1      (0)/(0)  626 ATCATTTGTTTTG / AACACCTGGTGCG
   651  S     cg060109r1      (0)/(0)  649 ATTC / AGCC
   657  S     cg060109r1      (0)/(0)  656 ATC / ACC
   667  I     cg060109r1      (0)/(0)  664 GTATT / GAAAAT
   679  S     cg060109r1      (0)/(0)  678 CTC / CAC
   692  S     cg060109r1      (0)/(0)  689 AAGTC / ATACC
   697  S     cg060109r1      (0)/(0)  695 GGCA / GTTA
   703  I     cg060109r1      (0)/(0)  703 CT / CTT
   707  I     cg060109r1      (0)/(0)  707 GT / GTT
   713  S     cg060109r1      (0)/(0)  712 CTG / CCG
   728  S     cg060109r1      (0)/(0)  727 TAT / TTT
   741  S     cg060109r1      (0)/(0)  734 CAGTCCGGT / CTGCTCTGTT
   745  S     cg060109r1      (0)/(0)  744 GGT / GTT

0 HQ discrepancies in 0 reads.
14 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 6.  2 reads; 361 bp (untrimmed), 361 (trimmed).
C  -618   410 cc090109r1    348 (324)  0.55 0.28 0.00  619 (627)   49 ( 49) 
    -11  1013 cc090109f1    352 (334)  0.28 0.00 0.00   15 ( 20)  652 (652) 

Overall discrep rates (%):             0.42 0.14 0.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90     186  51.5     186  51.5    0.00
 89       5   1.4     191  52.9    0.00
 88       4   1.1     195  54.0    0.00
 87       4   1.1     199  55.1    0.00
 86       5   1.4     204  56.5    0.00
 85      19   5.3     223  61.8    0.00
 84      13   3.6     236  65.4    0.00
 83      10   2.8     246  68.1    0.00
 82      14   3.9     260  72.0    0.00
 81       1   0.3     261  72.3    0.00
 80       4   1.1     265  73.4    0.00
 79       6   1.7     271  75.1    0.00
 78       8   2.2     279  77.3    0.00
 77      12   3.3     291  80.6    0.00
 76       6   1.7     297  82.3    0.00
 75       3   0.8     300  83.1    0.00
 74       1   0.3     301  83.4    0.00
 73       1   0.3     302  83.7    0.00
 72       4   1.1     306  84.8    0.00
 71      16   4.4     322  89.2    0.00
 70       2   0.6     324  89.8    0.00
 69       1   0.3     325  90.0    0.00
 68       3   0.8     328  90.9    0.00
 67       1   0.3     329  91.1    0.00
 65       3   0.8     332  92.0    0.00
 62       1   0.3     333  92.2    0.00
 61       1   0.3     334  92.5    0.00
 60       1   0.3     335  92.8    0.00
 59       3   0.8     338  93.6    0.00
 58       1   0.3     339  93.9    0.00
 57       3   0.8     342  94.7    0.00
 56       2   0.6     344  95.3    0.00
 50       1   0.3     345  95.6    0.00
 45       1   0.3     346  95.8    0.00
 44       3   0.8     349  96.7    0.00
 43       1   0.3     350  97.0    0.00
 42       7   1.9     357  98.9    0.00
 41       4   1.1     361 100.0    0.00   (quality -1 = terminal quality 0)

Avg. full length: 361.0, trimmed (qual > -1): 361.0
Avg. quality: 82.5 per base

Initial, terminal qual 0 segments:  (None), (None)

Regions of LLR- adjusted quality < 2.0:


1 regions, avg size 0.0, avg spacing 361.0

First_start: 9, last_end: 361

Slack, # used pairs (max_score), unused
 0     1  ( 7.7)     0 ( 0.0)        1

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     3        3+
  362 - right        0+      cc090109f1   ( -11)    No            372+

Bottom strand: 
 left -     0        0+      cc090109r1   ( 410)    Yes           410+
  362 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56    216    216    720 (100.00)     0  0    0   0   0   0     0 (0.00)    0    4 (0.56)
51     44    260    504 ( 70.00)     0  0    0   0   0   0     0 (0.00)    0    4 (0.79)
50     44    304    460 ( 63.89)     0  0    0   0   0   0     0 (0.00)    0    4 (0.87)
48      2    306    416 ( 57.78)     0  0    0   0   0   0     0 (0.00)    0    4 (0.96)
47     11    317    414 ( 57.50)     0  0    0   0   0   0     0 (0.00)    0    4 (0.97)
46     11    328    403 ( 55.97)     0  0    0   0   0   0     0 (0.00)    0    4 (0.99)
45      8    336    392 ( 54.44)     0  0    0   0   0   0     0 (0.00)    0    4 (1.02)
44     26    362    384 ( 53.33)     0  0    0   0   0   0     0 (0.00)    0    4 (1.04)
43     57    419    358 ( 49.72)     0  0    0   0   0   0     0 (0.00)    0    4 (1.12)
42    120    539    301 ( 41.81)     0  0    0   0   0   0     0 (0.00)    0    4 (1.33)
41     12    551    181 ( 25.14)     0  0    0   0   0   0     0 (0.00)    0    4 (2.21)
40     32    583    169 ( 23.47)     0  0    0   0   0   0     0 (0.00)    0    4 (2.37)
38      4    587    137 ( 19.03)     0  0    0   0   0   0     0 (0.00)    0    4 (2.92)
37     15    602    133 ( 18.47)     0  0    0   0   0   0     0 (0.00)    0    4 (3.01)
36      1    603    118 ( 16.39)     0  0    0   0   0   0     0 (0.00)    0    4 (3.39)
35     27    630    117 ( 16.25)     0  0    0   0   0   0     0 (0.00)    0    4 (3.42)
34      9    639     90 ( 12.50)     0  0    0   0   0   0     0 (0.00)    0    4 (4.44)
33      8    647     81 ( 11.25)     0  0    0   0   0   0     0 (0.00)    0    4 (4.94)
32      4    651     73 ( 10.14)     0  0    0   0   0   0     0 (0.00)    0    4 (5.48)
31      4    655     69 (  9.58)     0  0    0   0   0   0     0 (0.00)    0    4 (5.80)
30      1    656     65 (  9.03)     0  0    0   0   0   0     0 (0.00)    0    4 (6.15)
29      9    665     64 (  8.89)     0  0    0   0   0   0     0 (0.00)    0    4 (6.25)
28      6    671     55 (  7.64)     0  0    0   0   0   0     0 (0.00)    0    4 (7.27)
27      9    680     49 (  6.81)     0  0    0   0   0   0     0 (0.00)    0    4 (8.16)
25      2    682     40 (  5.56)     0  0    0   0   0   0     0 (0.00)    0    4 (10.00)
24      1    683     38 (  5.28)     0  0    0   0   0   0     0 (0.00)    0    4 (10.53)
23      3    686     37 (  5.14)     0  0    0   0   0   0     0 (0.00)    0    4 (10.81)
22      2    688     34 (  4.72)     0  0    0   0   0   0     0 (0.00)    0    4 (11.76)
21      2    690     32 (  4.44)     0  0    0   0   0   0     0 (0.00)    0    4 (12.50)
19      5    695     30 (  4.17)     0  0    0   0   0   0     0 (0.00)    0    4 (13.33)
17      2    697     25 (  3.47)     0  0    0   0   0   0     0 (0.00)    0    4 (16.00)
16      3    700     23 (  3.19)     0  0    0   0   0   0     0 (0.00)    0    4 (17.39)
15      2    702     20 (  2.78)     0  0    0   0   0   0     0 (0.00)    0    4 (20.00)
14      2    704     18 (  2.50)     0  0    0   0   0   0     0 (0.00)    0    4 (22.22)
12      2    706     16 (  2.22)     0  0    0   0   0   0     0 (0.00)    0    4 (25.00)
11      1    707     14 (  1.94)     0  0    0   1   0   0     1 (100.00)    1    4 (28.57)
10      2    709     13 (  1.81)     0  0    0   0   0   0     0 (0.00)    1    3 (23.08)
 9      7    716     11 (  1.53)     0  0    0   2   0   0     2 (28.57)    3    3 (27.27)
 8      3    719      4 (  0.56)     0  0    0   0   1   0     1 (33.33)    4    1 (25.00)
 7      1    720      1 (  0.14)     0  0    0   0   0   0     0 (0.00)    4    0 (0.00)
-1      0    720      0 (  0.00)     3  0    0   0   0   0     0 (0.00)    4    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90    372    372    715 (100.00)     0  0    0   0   0   0     0 (0.00)    0    3 (0.42)
89     10    382    343 ( 47.97)     0  0    0   0   0   0     0 (0.00)    0    3 (0.87)
88      8    390    333 ( 46.57)     0  0    0   0   0   0     0 (0.00)    0    3 (0.90)
87      8    398    325 ( 45.45)     0  0    0   0   0   0     0 (0.00)    0    3 (0.92)
86     10    408    317 ( 44.34)     0  0    0   0   0   0     0 (0.00)    0    3 (0.95)
85     38    446    307 ( 42.94)     0  0    0   0   0   0     0 (0.00)    0    3 (0.98)
84     26    472    269 ( 37.62)     0  0    0   0   0   0     0 (0.00)    0    3 (1.12)
83     20    492    243 ( 33.99)     0  0    0   0   0   0     0 (0.00)    0    3 (1.23)
82     28    520    223 ( 31.19)     0  0    0   0   0   0     0 (0.00)    0    3 (1.35)
81      2    522    195 ( 27.27)     0  0    0   0   0   0     0 (0.00)    0    3 (1.54)
80      8    530    193 ( 26.99)     0  0    0   0   0   0     0 (0.00)    0    3 (1.55)
79     12    542    185 ( 25.87)     0  0    0   0   0   0     0 (0.00)    0    3 (1.62)
78     16    558    173 ( 24.20)     0  0    0   0   0   0     0 (0.00)    0    3 (1.73)
77     24    582    157 ( 21.96)     0  0    0   0   0   0     0 (0.00)    0    3 (1.91)
76     12    594    133 ( 18.60)     0  0    0   0   0   0     0 (0.00)    0    3 (2.26)
75      6    600    121 ( 16.92)     0  0    0   0   0   0     0 (0.00)    0    3 (2.48)
74      2    602    115 ( 16.08)     0  0    0   0   0   0     0 (0.00)    0    3 (2.61)
73      2    604    113 ( 15.80)     0  0    0   0   0   0     0 (0.00)    0    3 (2.65)
72      8    612    111 ( 15.52)     0  0    0   0   0   0     0 (0.00)    0    3 (2.70)
71     22    634    103 ( 14.41)     0  0    0   0   0   0     0 (0.00)    0    3 (2.91)
70      6    640     81 ( 11.33)     0  0    0   0   0   0     0 (0.00)    0    3 (3.70)
69      2    642     75 ( 10.49)     0  0    0   0   0   0     0 (0.00)    0    3 (4.00)
68      6    648     73 ( 10.21)     0  0    0   0   0   0     0 (0.00)    0    3 (4.11)
67      2    650     67 (  9.37)     0  0    0   0   0   0     0 (0.00)    0    3 (4.48)
65      4    654     65 (  9.09)     0  0    0   0   0   0     0 (0.00)    0    3 (4.62)
64      2    656     61 (  8.53)     0  0    0   0   0   0     0 (0.00)    0    3 (4.92)
63      1    657     59 (  8.25)     0  0    0   0   0   0     0 (0.00)    0    3 (5.08)
62      2    659     58 (  8.11)     0  0    0   0   0   0     0 (0.00)    0    3 (5.17)
61      2    661     56 (  7.83)     0  0    0   0   0   0     0 (0.00)    0    3 (5.36)
60      2    663     54 (  7.55)     0  0    0   0   0   0     0 (0.00)    0    3 (5.56)
59      4    667     52 (  7.27)     0  0    0   0   0   0     0 (0.00)    0    3 (5.77)
58      1    668     48 (  6.71)     0  0    0   0   0   0     0 (0.00)    0    3 (6.25)
57      3    671     47 (  6.57)     0  0    0   0   0   0     0 (0.00)    0    3 (6.38)
56      3    674     44 (  6.15)     0  0    0   0   0   0     0 (0.00)    0    3 (6.82)
55      4    678     41 (  5.73)     0  0    0   0   0   0     0 (0.00)    0    3 (7.32)
53      1    679     37 (  5.17)     0  0    0   0   0   0     0 (0.00)    0    3 (8.11)
50      2    681     36 (  5.03)     0  0    0   0   0   0     0 (0.00)    0    3 (8.33)
45      1    682     34 (  4.76)     0  0    0   0   0   0     0 (0.00)    0    3 (8.82)
44      4    686     33 (  4.62)     0  0    0   0   0   0     0 (0.00)    0    3 (9.09)
43      3    689     29 (  4.06)     0  0    0   0   0   0     0 (0.00)    0    3 (10.34)
42     10    699     26 (  3.64)     0  0    0   0   0   0     0 (0.00)    0    3 (11.54)
41      4    703     16 (  2.24)     0  0    0   0   0   0     0 (0.00)    0    3 (18.75)
38      1    704     12 (  1.68)     0  0    0   0   0   0     0 (0.00)    0    3 (25.00)
37      1    705     11 (  1.54)     0  0    0   0   0   0     0 (0.00)    0    3 (27.27)
30      1    706     10 (  1.40)     0  0    0   0   0   0     0 (0.00)    0    3 (30.00)
17      1    707      9 (  1.26)     0  0    0   0   0   0     0 (0.00)    0    3 (33.33)
10      1    708      8 (  1.12)     0  0    0   0   0   0     0 (0.00)    0    3 (37.50)
 9      5    713      7 (  0.98)     0  0    0   2   0   0     2 (40.00)    2    3 (42.86)
 8      1    714      2 (  0.28)     0  0    0   0   1   0     1 (100.00)    3    1 (50.00)
 7      1    715      1 (  0.14)     0  0    0   0   0   0     0 (0.00)    3    0 (0.00)
-1      5    720      0 (  0.00)     3  0    0   1   0   0     1 (20.00)    4    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
 41       4        4        2
 42       7       11        4
 43       1       12        3
 44       3       15        4
 45       1       16        3
 50       1       17        3
 56       2       19        4
 57       3       22        5
 58       1       23        5
 59       3       26        6
 60       1       27        5
 61       1       28        6
 62       1       29        6
 65       3       32        7
 67       1       33        6
 68       3       36        7
 69       1       37        8
 70       2       39        9
 71      16       55        9
 72       4       59        9
 73       1       60        8
 74       1       61        9
 75       3       64        9
 76       6       70       11
 77      12       82       17
 78       8       90       15
 79       6       96       16
 80       4      100       18
 81       1      101       17
 82      14      115       18
 83      10      125       17
 84      13      138       16
 85      19      157       23
 86       5      162       21
 87       4      166       22
 88       4      170       22
 89       5      175       24
 90     186      361        1

SS region: 3 (0.83%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
  361     -4.2  [-4.2,  0.0]  (0, 1)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:   E 9- 361

Contig 7.  2 reads; 1006 bp (untrimmed), 872 (trimmed).  Isolated contig.
      0  1006 dg110109r1    955 (  0)  0.70 0.40 0.00    8 ( 15)    0 (121) 
      1  1001 bg110109r1    910 (  0)  1.61 0.00 0.60    0 ( 14)    8 (109) 

Overall discrep rates (%):             1.15 0.20 0.30

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 66     206  20.5     206  20.5    0.00
 61      24   2.4     230  22.9    0.00
 60      91   9.0     321  31.9    0.00
 58       2   0.2     323  32.1    0.00
 57       6   0.6     329  32.7    0.00
 56      14   1.4     343  34.1    0.00
 55       1   0.1     344  34.2    0.00
 54      42   4.2     386  38.4    0.00
 53      24   2.4     410  40.8    0.00
 52      83   8.3     493  49.0    0.00
 51      11   1.1     504  50.1    0.00
 50      39   3.9     543  54.0    0.00
 48       7   0.7     550  54.7    0.00
 47      21   2.1     571  56.8    0.00
 46       2   0.2     573  57.0    0.00
 45      18   1.8     591  58.7    0.00
 44       8   0.8     599  59.5    0.00
 43       8   0.8     607  60.3    0.00
 42       3   0.3     610  60.6    0.00
 41       4   0.4     614  61.0    0.00
 40       6   0.6     620  61.6    0.00
 39      18   1.8     638  63.4    0.01
 38       2   0.2     640  63.6    0.01
 37       5   0.5     645  64.1    0.01
 36       4   0.4     649  64.5    0.01
 35       7   0.7     656  65.2    0.01
 34       7   0.7     663  65.9    0.01
 33       5   0.5     668  66.4    0.02
 32       6   0.6     674  67.0    0.02
 31       8   0.8     682  67.8    0.03
 30       3   0.3     685  68.1    0.03
 29       5   0.5     690  68.6    0.04
 28       2   0.2     692  68.8    0.04
 27       5   0.5     697  69.3    0.05
 26       4   0.4     701  69.7    0.06
 25      12   1.2     713  70.9    0.10
 24       9   0.9     722  71.8    0.13
 23       3   0.3     725  72.1    0.15
 22       3   0.3     728  72.4    0.17
 21       6   0.6     734  73.0    0.21
 20       3   0.3     737  73.3    0.24
 19       1   0.1     738  73.4    0.26
 18       3   0.3     741  73.7    0.30
 17       5   0.5     746  74.2    0.40
 16      11   1.1     757  75.2    0.68
 15      26   2.6     783  77.8    1.50
 14       8   0.8     791  78.6    1.82
 13      10   1.0     801  79.6    2.32
 12       8   0.8     809  80.4    2.83
 11      10   1.0     819  81.4    3.62
 10      17   1.7     836  83.1    5.32
  9      13   1.3     849  84.4    6.96
  8      22   2.2     871  86.6   10.45
  7       1   0.1     872  86.7   10.64
 -1     134  13.3    1006 100.0  144.64   (quality -1 = terminal quality 0)

Avg. full length: 1006.0, trimmed (qual > -1): 872.0
Avg. quality: 40.6 per base

Initial, terminal qual 0 segments:  1-14, 887-1006

Regions of LLR- adjusted quality < 2.0:
1-19, 22, 39-41, 75-80, 660, 713-714, 724-725, 732, 
737-739, 742-744, 746, 756-761, 764-773, 775, 781-784, 786-792, 
799-805, 809-824, 826-850, 856-1006, 

20 regions, avg size 13.4, avg spacing 50.3

First_start: 15, last_end: 892

Slack, # used pairs (max_score), unused
 0     0  ( 0.0)     0 ( 0.0)        1
 2     1  (21.0)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 1007 - right        0+      bg110109r1   (   1)    No           1005+

Bottom strand: 
 left - right     1006+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56    206    206   1970 (100.00)     0  0    0   0   0   0     0 (0.00)    0   33 (1.68)
51     24    230   1764 ( 89.54)     0  0    0   0   0   0     0 (0.00)    0   33 (1.87)
50    110    340   1740 ( 88.32)     0  0    0   0   0   0     0 (0.00)    0   33 (1.90)
48      2    342   1630 ( 82.74)     0  0    0   0   0   0     0 (0.00)    0   33 (2.02)
47     11    353   1628 ( 82.64)     0  0    0   0   0   0     0 (0.00)    0   33 (2.03)
46     15    368   1617 ( 82.08)     0  0    0   0   0   0     0 (0.00)    0   33 (2.04)
45      1    369   1602 ( 81.32)     0  0    0   0   0   0     0 (0.00)    0   33 (2.06)
44     88    457   1601 ( 81.27)     0  0    0   0   0   0     0 (0.00)    0   33 (2.06)
43     26    483   1513 ( 76.80)     0  0    0   0   0   0     0 (0.00)    0   33 (2.18)
42    135    618   1487 ( 75.48)     0  0    0   0   0   0     0 (0.00)    0   33 (2.22)
41     26    644   1352 ( 68.63)     0  0    0   0   0   0     0 (0.00)    0   33 (2.44)
40     52    696   1326 ( 67.31)     0  0    0   0   0   0     0 (0.00)    0   33 (2.49)
39      6    702   1274 ( 64.67)     0  0    0   0   0   0     0 (0.00)    0   33 (2.59)
38      8    710   1268 ( 64.37)     0  0    0   0   0   0     0 (0.00)    0   33 (2.60)
37    105    815   1260 ( 63.96)     0  0    0   0   0   0     0 (0.00)    0   33 (2.62)
36      3    818   1155 ( 58.63)     0  0    0   0   0   0     0 (0.00)    0   33 (2.86)
35    112    930   1152 ( 58.48)     0  0    0   0   0   0     0 (0.00)    0   33 (2.86)
34     14    944   1040 ( 52.79)     0  0    0   0   0   0     0 (0.00)    0   33 (3.17)
33     80   1024   1026 ( 52.08)     0  0    0   0   0   0     0 (0.00)    0   33 (3.22)
32     15   1039    946 ( 48.02)     0  0    0   0   0   0     0 (0.00)    0   33 (3.49)
31     13   1052    931 ( 47.26)     0  0    0   0   0   0     0 (0.00)    0   33 (3.54)
30     26   1078    918 ( 46.60)     0  0    0   0   0   0     0 (0.00)    0   33 (3.59)
29     48   1126    892 ( 45.28)     0  0    0   0   0   0     0 (0.00)    0   33 (3.70)
28     13   1139    844 ( 42.84)     0  0    0   0   0   0     0 (0.00)    0   33 (3.91)
27     34   1173    831 ( 42.18)     0  0    0   0   0   0     0 (0.00)    0   33 (3.97)
26     16   1189    797 ( 40.46)     0  0    0   0   0   0     0 (0.00)    0   33 (4.14)
25     27   1216    781 ( 39.64)     0  0    0   0   0   0     0 (0.00)    0   33 (4.23)
24     35   1251    754 ( 38.27)     0  0    0   0   0   0     0 (0.00)    0   33 (4.38)
23     21   1272    719 ( 36.50)     0  0    0   0   0   0     0 (0.00)    0   33 (4.59)
22     30   1302    698 ( 35.43)     0  0    0   0   0   0     0 (0.00)    0   33 (4.73)
21     31   1333    668 ( 33.91)     0  0    0   1   0   0     1 (3.23)    1   33 (4.94)
20     12   1345    637 ( 32.34)     0  0    0   0   0   0     0 (0.00)    1   32 (5.02)
19     27   1372    625 ( 31.73)     0  0    0   0   0   0     0 (0.00)    1   32 (5.12)
18     13   1385    598 ( 30.36)     0  0    0   0   0   0     0 (0.00)    1   32 (5.35)
17     18   1403    585 ( 29.70)     0  0    0   0   0   0     0 (0.00)    1   32 (5.47)
16     24   1427    567 ( 28.78)     0  0    0   0   0   0     0 (0.00)    1   32 (5.64)
15     32   1459    543 ( 27.56)     0  0    0   0   0   0     0 (0.00)    1   32 (5.89)
14     28   1487    511 ( 25.94)     0  0    0   0   0   0     0 (0.00)    1   32 (6.26)
13     39   1526    483 ( 24.52)     0  0    0   0   1   1     2 (5.13)    3   32 (6.63)
12     35   1561    444 ( 22.54)     0  0    0   1   0   0     1 (2.86)    4   30 (6.76)
11     53   1614    409 ( 20.76)     0  0    0   1   0   0     1 (1.89)    5   29 (7.09)
10     69   1683    356 ( 18.07)     0  0    0   5   0   1     6 (8.70)   11   28 (7.87)
 9     95   1778    287 ( 14.57)     0  0    0   5   0   1     6 (6.32)   17   22 (7.67)
 8     90   1868    192 (  9.75)     0  0    0   3   1   1     5 (5.56)   22   16 (8.33)
 7     56   1924    102 (  5.18)     0  0    0   2   0   0     2 (3.57)   24   11 (10.78)
 6     46   1970     46 (  2.34)     0  0    0   5   2   2     9 (19.57)   33    9 (19.57)
-1     20   1990      0 (  0.00)    15  0    0   0   0   0     0 (0.00)   33    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
66    407    407   1747 (100.00)     0  0    0   0   0   0     0 (0.00)    0    9 (0.52)
61     48    455   1340 ( 76.70)     0  0    0   0   0   0     0 (0.00)    0    9 (0.67)
60    181    636   1292 ( 73.96)     0  0    0   0   0   0     0 (0.00)    0    9 (0.70)
58      4    640   1111 ( 63.59)     0  0    0   0   0   0     0 (0.00)    0    9 (0.81)
57     11    651   1107 ( 63.37)     0  0    0   0   0   0     0 (0.00)    0    9 (0.81)
56     28    679   1096 ( 62.74)     0  0    0   0   0   0     0 (0.00)    0    9 (0.82)
55      2    681   1068 ( 61.13)     0  0    0   0   0   0     0 (0.00)    0    9 (0.84)
54     82    763   1066 ( 61.02)     0  0    0   0   0   0     0 (0.00)    0    9 (0.84)
53     48    811    984 ( 56.33)     0  0    0   0   0   0     0 (0.00)    0    9 (0.91)
52    166    977    936 ( 53.58)     0  0    0   0   0   0     0 (0.00)    0    9 (0.96)
51     22    999    770 ( 44.08)     0  0    0   0   0   0     0 (0.00)    0    9 (1.17)
50     73   1072    748 ( 42.82)     0  0    0   0   0   0     0 (0.00)    0    9 (1.20)
48     14   1086    675 ( 38.64)     0  0    0   0   0   0     0 (0.00)    0    9 (1.33)
47     42   1128    661 ( 37.84)     0  0    0   0   0   0     0 (0.00)    0    9 (1.36)
46      4   1132    619 ( 35.43)     0  0    0   0   0   0     0 (0.00)    0    9 (1.45)
45     35   1167    615 ( 35.20)     0  0    0   0   0   0     0 (0.00)    0    9 (1.46)
44     13   1180    580 ( 33.20)     0  0    0   0   0   0     0 (0.00)    0    9 (1.55)
43     15   1195    567 ( 32.46)     0  0    0   0   0   0     0 (0.00)    0    9 (1.59)
42      6   1201    552 ( 31.60)     0  0    0   0   0   0     0 (0.00)    0    9 (1.63)
41      7   1208    546 ( 31.25)     0  0    0   0   0   0     0 (0.00)    0    9 (1.65)
40      7   1215    539 ( 30.85)     0  0    0   0   0   0     0 (0.00)    0    9 (1.67)
39     32   1247    532 ( 30.45)     0  0    0   0   0   0     0 (0.00)    0    9 (1.69)
38      5   1252    500 ( 28.62)     0  0    0   0   0   0     0 (0.00)    0    9 (1.80)
37      7   1259    495 ( 28.33)     0  0    0   0   0   0     0 (0.00)    0    9 (1.82)
36      7   1266    488 ( 27.93)     0  0    0   0   0   0     0 (0.00)    0    9 (1.84)
35     10   1276    481 ( 27.53)     0  0    0   0   0   0     0 (0.00)    0    9 (1.87)
34     11   1287    471 ( 26.96)     0  0    0   0   0   0     0 (0.00)    0    9 (1.91)
33      8   1295    460 ( 26.33)     0  0    0   0   0   0     0 (0.00)    0    9 (1.96)
32     11   1306    452 ( 25.87)     0  0    0   0   0   0     0 (0.00)    0    9 (1.99)
31     11   1317    441 ( 25.24)     0  0    0   0   0   0     0 (0.00)    0    9 (2.04)
30      6   1323    430 ( 24.61)     0  0    0   0   0   0     0 (0.00)    0    9 (2.09)
29     12   1335    424 ( 24.27)     0  0    0   0   0   0     0 (0.00)    0    9 (2.12)
28      3   1338    412 ( 23.58)     0  0    0   0   0   0     0 (0.00)    0    9 (2.18)
27      9   1347    409 ( 23.41)     0  0    0   0   0   0     0 (0.00)    0    9 (2.20)
26      9   1356    400 ( 22.90)     0  0    0   0   0   0     0 (0.00)    0    9 (2.25)
25     20   1376    391 ( 22.38)     0  0    0   0   0   0     0 (0.00)    0    9 (2.30)
24     22   1398    371 ( 21.24)     0  0    0   0   0   0     0 (0.00)    0    9 (2.43)
23      5   1403    349 ( 19.98)     0  0    0   0   0   0     0 (0.00)    0    9 (2.58)
22      9   1412    344 ( 19.69)     0  0    0   0   0   0     0 (0.00)    0    9 (2.62)
21     14   1426    335 ( 19.18)     0  0    0   0   0   0     0 (0.00)    0    9 (2.69)
20      4   1430    321 ( 18.37)     0  0    0   0   0   0     0 (0.00)    0    9 (2.80)
19      7   1437    317 ( 18.15)     0  0    0   0   0   0     0 (0.00)    0    9 (2.84)
18      6   1443    310 ( 17.74)     0  0    0   0   0   0     0 (0.00)    0    9 (2.90)
17      9   1452    304 ( 17.40)     0  0    0   0   0   0     0 (0.00)    0    9 (2.96)
16     16   1468    295 ( 16.89)     0  0    0   0   0   0     0 (0.00)    0    9 (3.05)
15     38   1506    279 ( 15.97)     0  0    0   0   0   0     0 (0.00)    0    9 (3.23)
14     17   1523    241 ( 13.80)     0  0    0   0   0   0     0 (0.00)    0    9 (3.73)
13     19   1542    224 ( 12.82)     0  0    0   0   1   0     1 (5.26)    1    9 (4.02)
12     18   1560    205 ( 11.73)     0  0    0   0   0   0     0 (0.00)    1    8 (3.90)
11     26   1586    187 ( 10.70)     0  0    0   0   0   0     0 (0.00)    1    8 (4.28)
10     38   1624    161 (  9.22)     0  0    0   2   0   0     2 (5.26)    3    8 (4.97)
 9     39   1663    123 (  7.04)     0  0    0   1   0   0     1 (2.56)    4    6 (4.88)
 8     40   1703     84 (  4.81)     0  0    0   1   1   0     2 (5.00)    6    5 (5.95)
 7     28   1731     44 (  2.52)     0  0    0   0   0   0     0 (0.00)    6    3 (6.82)
 6     16   1747     16 (  0.92)     0  0    0   2   1   0     3 (18.75)    9    3 (18.75)
-1    243   1990      0 (  0.00)    15  0    0  17   1   6    24 (9.88)   33    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     134      134        2
  7       1      135        3
  8      22      157       11
  9      13      170       13
 10      17      187       13
 11      10      197       18
 12       8      205       18
 13      10      215       19
 14       8      223       18
 15      26      249       24
 16      11      260       20
 17       5      265       19
 18       3      268       19
 19       1      269       20
 20       3      272       19
 21       6      278       18
 22       3      281       17
 23       3      284       17
 24       9      293       18
 25      12      305       17
 26       4      309       16
 27       5      314       16
 28       2      316       14
 29       5      321       14
 30       3      324       15
 31       8      332       14
 32       6      338       14
 33       5      343       13
 34       7      350       14
 35       7      357       14
 36       4      361       13
 37       5      366       14
 38       2      368       14
 39      18      386       12
 40       6      392       14
 41       4      396       13
 42       3      399       12
 43       8      407       10
 44       8      415       11
 45      18      433       12
 46       2      435       13
 47      21      456       16
 48       7      463       19
 50      39      502       20
 51      11      513       23
 52      83      596       34
 53      24      620       33
 54      42      662       41
 55       1      663       41
 56      14      677       37
 57       6      683       38
 58       2      685       36
 60      91      776       41
 61      24      800       41
 66     206     1006        1

SS region: 1006 (100.00%), flagged: 1 (0.10%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality):
   891  S     bg110109r1      (0)/(0)  890 AAA / ATA
   906  D     bg110109r1      (0)/(0)  894 TTAATACATAAAGA / TAAAAAAAAAAAA
   912  S     bg110109r1      (0)/(0)  911 AAA / AGA
   925  D     bg110109r1      (0)/(0)  923 GGGT / GGT
   932  S     bg110109r1      (0)/(0)  931 ATG / AGG
   939  S     bg110109r1      (0)/(0)  938 CCT / CTT
   944  S     bg110109r1      (0)/(0)  942 TTTT / TCAT
   957  D     bg110109r1      (0)/(0)  955 TTTG / TGG
   964  D     bg110109r1      (0)/(0)  962 TTTA / TTA
   974  D     bg110109r1      (0)/(0)  967 CCCCTGCGA / CGCTTCCA
   984  D     bg110109r1      (0)/(0)  982 AACC / AAC

0 HQ discrepancies in 0 reads.
11 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 8.  2 reads; 34 bp (untrimmed), 0 (trimmed).  Isolated contig.
    -18  1022 ch040109r1     30 (  0)  2.94 0.00 0.00   19 ( 19)  988 (988) 
    -12   971 ed020109r1     32 (  0)  0.00 0.00 0.00   13 ( 13)  937 (937) 

Overall discrep rates (%):             1.47 0.00 0.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 -1      34 100.0      34 100.0   34.00   (quality -1 = terminal quality 0)

Avg. full length: 34.0, trimmed (qual > -1): 0.0
Avg. quality: 0.0 per base

Initial, terminal qual 0 segments:  1-34, (None)

Regions of LLR- adjusted quality < 2.0:
1-34, 

1 regions, avg size 34.0, avg spacing 34.0

First_start: 1, last_end: 34

Slack, # used pairs (max_score), unused
 0     1  ( 0.0)     0 ( 0.0)        1

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
   35 - right        0+      ed020109r1   ( -12)    No             46+

Bottom strand: 
 left - right       34+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
37      2      2     68 (100.00)     0  0    0   0   0   0     0 (0.00)    0    1 (1.47)
35      1      3     66 ( 97.06)     0  0    0   0   0   0     0 (0.00)    0    1 (1.52)
33      1      4     65 ( 95.59)     0  0    0   0   0   0     0 (0.00)    0    1 (1.54)
32      1      5     64 ( 94.12)     0  0    0   0   0   0     0 (0.00)    0    1 (1.56)
29      1      6     63 ( 92.65)     0  0    0   0   0   0     0 (0.00)    0    1 (1.59)
27      3      9     62 ( 91.18)     0  0    0   0   0   0     0 (0.00)    0    1 (1.61)
26      2     11     59 ( 86.76)     0  0    0   0   0   0     0 (0.00)    0    1 (1.69)
25      3     14     57 ( 83.82)     0  0    0   0   0   0     0 (0.00)    0    1 (1.75)
24      4     18     54 ( 79.41)     0  0    0   0   0   0     0 (0.00)    0    1 (1.85)
22      5     23     50 ( 73.53)     0  0    0   0   0   0     0 (0.00)    0    1 (2.00)
21      1     24     45 ( 66.18)     0  0    0   0   0   0     0 (0.00)    0    1 (2.22)
20      1     25     44 ( 64.71)     0  0    0   0   0   0     0 (0.00)    0    1 (2.27)
19      3     28     43 ( 63.24)     0  0    0   0   0   0     0 (0.00)    0    1 (2.33)
18      1     29     40 ( 58.82)     0  0    0   0   0   0     0 (0.00)    0    1 (2.50)
16      4     33     39 ( 57.35)     0  0    0   0   0   0     0 (0.00)    0    1 (2.56)
15      3     36     35 ( 51.47)     0  0    0   0   0   0     0 (0.00)    0    1 (2.86)
14      1     37     32 ( 47.06)     0  0    0   0   0   0     0 (0.00)    0    1 (3.12)
13      5     42     31 ( 45.59)     0  0    0   0   0   0     0 (0.00)    0    1 (3.23)
12      2     44     26 ( 38.24)     0  0    0   0   0   0     0 (0.00)    0    1 (3.85)
11      3     47     24 ( 35.29)     0  0    0   0   0   0     0 (0.00)    0    1 (4.17)
10      6     53     21 ( 30.88)     0  0    0   0   0   0     0 (0.00)    0    1 (4.76)
 9      7     60     15 ( 22.06)     0  0    0   0   0   0     0 (0.00)    0    1 (6.67)
 8      4     64      8 ( 11.76)     0  0    0   0   0   0     0 (0.00)    0    1 (12.50)
 6      4     68      4 (  5.88)     0  0    0   1   0   0     1 (25.00)    1    1 (25.00)
-1      0     68      0 (  0.00)     0  0    0   0   0   0     0 (0.00)    1    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
-1     68     68      0 (  0.00)     0  0    0   1   0   0     1 (1.47)    1    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      34       34        1

SS region: 34 (100.00%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality):
    12  S     ch040109r1      (0)/(0)  11 CCG / CTG

0 HQ discrepancies in 0 reads.
1 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 9.  2 reads; 1033 bp (untrimmed), 783 (trimmed).  Isolated contig.
      1   996 bg110109f1    830 (  0)  1.22 0.11 0.77    0 ( 40)   92 (168) 
      9  1033 dg110109f1    965 (  0)  0.99 0.10 0.20   15 ( 31)    0 (210) 

Overall discrep rates (%):             1.10 0.10 0.47

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 66      49   4.7      49   4.7    0.00
 60     102   9.9     151  14.6    0.00
 57       6   0.6     157  15.2    0.00
 56       2   0.2     159  15.4    0.00
 55       1   0.1     160  15.5    0.00
 54      83   8.0     243  23.5    0.00
 53      10   1.0     253  24.5    0.00
 52     116  11.2     369  35.7    0.00
 51      24   2.3     393  38.0    0.00
 50      14   1.4     407  39.4    0.00
 49       7   0.7     414  40.1    0.00
 48       5   0.5     419  40.6    0.00
 47      47   4.5     466  45.1    0.00
 46       4   0.4     470  45.5    0.00
 45      37   3.6     507  49.1    0.00
 44       1   0.1     508  49.2    0.00
 43      15   1.5     523  50.6    0.00
 42       5   0.5     528  51.1    0.01
 41      11   1.1     539  52.2    0.01
 40       8   0.8     547  53.0    0.01
 39      17   1.6     564  54.6    0.01
 38      13   1.3     577  55.9    0.01
 37      10   1.0     587  56.8    0.01
 36       4   0.4     591  57.2    0.01
 35       9   0.9     600  58.1    0.02
 34       8   0.8     608  58.9    0.02
 33       5   0.5     613  59.3    0.02
 32       4   0.4     617  59.7    0.02
 31       6   0.6     623  60.3    0.03
 30       1   0.1     624  60.4    0.03
 29      13   1.3     637  61.7    0.05
 28       3   0.3     640  62.0    0.05
 27       7   0.7     647  62.6    0.07
 26       1   0.1     648  62.7    0.07
 25       9   0.9     657  63.6    0.10
 24       2   0.2     659  63.8    0.10
 23       3   0.3     662  64.1    0.12
 22       4   0.4     666  64.5    0.15
 21      12   1.2     678  65.6    0.24
 20       6   0.6     684  66.2    0.30
 19      12   1.2     696  67.4    0.45
 18       4   0.4     700  67.8    0.51
 17       8   0.8     708  68.5    0.67
 16       7   0.7     715  69.2    0.85
 15      13   1.3     728  70.5    1.26
 14       9   0.9     737  71.3    1.62
 13       7   0.7     744  72.0    1.97
 12      10   1.0     754  73.0    2.60
 11       7   0.7     761  73.7    3.16
 10      10   1.0     771  74.6    4.16
  9       1   0.1     772  74.7    4.28
  8       7   0.7     779  75.4    5.39
  7       3   0.3     782  75.7    5.99
  6       1   0.1     783  75.8    6.24
 -1     250  24.2    1033 100.0  256.24   (quality -1 = terminal quality 0)

Avg. full length: 1033.0, trimmed (qual > -1): 783.0
Avg. quality: 33.6 per base

Initial, terminal qual 0 segments:  1-40, 824-1033

Regions of LLR- adjusted quality < 2.0:
1-41, 48-49, 53, 84-91, 669, 676-681, 711-714, 728-729, 
732, 737-741, 748-755, 757-775, 777-785, 788-791, 793, 795-807, 
810-1033, 

17 regions, avg size 20.5, avg spacing 60.8

First_start: 40, last_end: 828

Slack, # used pairs (max_score), unused
 0     0  ( 0.0)     0 ( 0.0)        1
 1     1  (17.4)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 1034 - right        0+      dg110109f1   (   9)    No           1024+

Bottom strand: 
 left - right     1033+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56     49     49   1755 (100.00)     0  0    0   0   0   0     0 (0.00)    0   32 (1.82)
50    108    157   1706 ( 97.21)     0  0    0   0   0   0     0 (0.00)    0   32 (1.88)
48      2    159   1598 ( 91.05)     0  0    0   0   0   0     0 (0.00)    0   32 (2.00)
47      7    166   1596 ( 90.94)     0  0    0   0   0   0     0 (0.00)    0   32 (2.01)
46      2    168   1589 ( 90.54)     0  0    0   0   0   0     0 (0.00)    0   32 (2.01)
45      1    169   1587 ( 90.43)     0  0    0   0   0   0     0 (0.00)    0   32 (2.02)
44    100    269   1586 ( 90.37)     0  0    0   0   0   0     0 (0.00)    0   32 (2.02)
43     11    280   1486 ( 84.67)     0  0    0   0   0   0     0 (0.00)    0   32 (2.15)
42    140    420   1475 ( 84.05)     0  0    0   0   0   0     0 (0.00)    0   32 (2.17)
41     30    450   1335 ( 76.07)     0  0    0   0   0   0     0 (0.00)    0   32 (2.40)
40     18    468   1305 ( 74.36)     0  0    0   0   0   0     0 (0.00)    0   32 (2.45)
39     10    478   1287 ( 73.33)     0  0    0   0   0   0     0 (0.00)    0   32 (2.49)
38      6    484   1277 ( 72.76)     0  0    0   0   0   0     0 (0.00)    0   32 (2.51)
37    128    612   1271 ( 72.42)     0  0    0   0   0   0     0 (0.00)    0   32 (2.52)
36      4    616   1143 ( 65.13)     0  0    0   0   0   0     0 (0.00)    0   32 (2.80)
35    107    723   1139 ( 64.90)     0  0    0   0   0   0     0 (0.00)    0   32 (2.81)
34      3    726   1032 ( 58.80)     0  0    0   0   0   0     0 (0.00)    0   32 (3.10)
33     99    825   1029 ( 58.63)     0  0    0   0   0   0     0 (0.00)    0   32 (3.11)
32     12    837    930 ( 52.99)     0  0    0   0   0   0     0 (0.00)    0   32 (3.44)
31     30    867    918 ( 52.31)     0  0    0   0   0   0     0 (0.00)    0   32 (3.49)
30     40    907    888 ( 50.60)     0  0    0   0   0   0     0 (0.00)    0   32 (3.60)
29     50    957    848 ( 48.32)     0  0    0   0   0   0     0 (0.00)    0   32 (3.77)
28     38    995    798 ( 45.47)     0  0    0   0   0   0     0 (0.00)    0   32 (4.01)
27     43   1038    760 ( 43.30)     0  0    0   0   0   0     0 (0.00)    0   32 (4.21)
26     12   1050    717 ( 40.85)     0  0    0   0   0   0     0 (0.00)    0   32 (4.46)
25     26   1076    705 ( 40.17)     0  0    0   0   0   0     0 (0.00)    0   32 (4.54)
24     21   1097    679 ( 38.69)     0  0    0   0   0   0     0 (0.00)    0   32 (4.71)
23     27   1124    658 ( 37.49)     0  0    0   0   0   0     0 (0.00)    0   32 (4.86)
22     35   1159    631 ( 35.95)     0  0    0   0   0   0     0 (0.00)    0   32 (5.07)
21     50   1209    596 ( 33.96)     0  0    0   0   0   0     0 (0.00)    0   32 (5.37)
20     16   1225    546 ( 31.11)     0  0    0   0   0   0     0 (0.00)    0   32 (5.86)
19     36   1261    530 ( 30.20)     0  0    0   0   0   0     0 (0.00)    0   32 (6.04)
18     24   1285    494 ( 28.15)     0  0    0   0   0   0     0 (0.00)    0   32 (6.48)
17     27   1312    470 ( 26.78)     0  0    0   0   0   0     0 (0.00)    0   32 (6.81)
16     17   1329    443 ( 25.24)     0  0    0   0   0   0     0 (0.00)    0   32 (7.22)
15     40   1369    426 ( 24.27)     0  0    0   0   0   0     0 (0.00)    0   32 (7.51)
14     23   1392    386 ( 21.99)     0  0    0   0   0   1     1 (4.35)    1   32 (8.29)
13     32   1424    363 ( 20.68)     0  0    0   1   0   0     1 (3.12)    2   31 (8.54)
12     36   1460    331 ( 18.86)     0  0    0   2   0   0     2 (5.56)    4   30 (9.06)
11     37   1497    295 ( 16.81)     0  0    0   0   0   1     1 (2.70)    5   28 (9.49)
10     55   1552    258 ( 14.70)     0  0    0   2   0   0     2 (3.64)    7   27 (10.47)
 9     73   1625    203 ( 11.57)     0  0    0   4   0   3     7 (9.59)   14   25 (12.32)
 8     58   1683    130 (  7.41)     0  0    0   5   2   2     9 (15.52)   23   18 (13.85)
 7     40   1723     72 (  4.10)     0  0    0   2   0   1     3 (7.50)   26    9 (12.50)
 6     30   1753     32 (  1.82)     0  0    0   4   0   1     5 (16.67)   31    6 (18.75)
 4      2   1755      2 (  0.11)     0  0    0   1   0   0     1 (50.00)   32    1 (50.00)
-1    152   1907      0 (  0.00)   107  0    0   0   0   0     0 (0.00)   32    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
66     98     98   1565 (100.00)     0  0    0   0   0   0     0 (0.00)    0   13 (0.83)
60    204    302   1467 ( 93.74)     0  0    0   0   0   0     0 (0.00)    0   13 (0.89)
57     12    314   1263 ( 80.70)     0  0    0   0   0   0     0 (0.00)    0   13 (1.03)
56      4    318   1251 ( 79.94)     0  0    0   0   0   0     0 (0.00)    0   13 (1.04)
55      2    320   1247 ( 79.68)     0  0    0   0   0   0     0 (0.00)    0   13 (1.04)
54    166    486   1245 ( 79.55)     0  0    0   0   0   0     0 (0.00)    0   13 (1.04)
53     20    506   1079 ( 68.95)     0  0    0   0   0   0     0 (0.00)    0   13 (1.20)
52    229    735   1059 ( 67.67)     0  0    0   0   0   0     0 (0.00)    0   13 (1.23)
51     48    783    830 ( 53.04)     0  0    0   0   0   0     0 (0.00)    0   13 (1.57)
50     26    809    782 ( 49.97)     0  0    0   0   0   0     0 (0.00)    0   13 (1.66)
49     14    823    756 ( 48.31)     0  0    0   0   0   0     0 (0.00)    0   13 (1.72)
48     10    833    742 ( 47.41)     0  0    0   0   0   0     0 (0.00)    0   13 (1.75)
47     92    925    732 ( 46.77)     0  0    0   0   0   0     0 (0.00)    0   13 (1.78)
46      8    933    640 ( 40.89)     0  0    0   0   0   0     0 (0.00)    0   13 (2.03)
45     70   1003    632 ( 40.38)     0  0    0   0   0   0     0 (0.00)    0   13 (2.06)
44      2   1005    562 ( 35.91)     0  0    0   0   0   0     0 (0.00)    0   13 (2.31)
43     23   1028    560 ( 35.78)     0  0    0   0   0   0     0 (0.00)    0   13 (2.32)
42      9   1037    537 ( 34.31)     0  0    0   0   0   0     0 (0.00)    0   13 (2.42)
41     15   1052    528 ( 33.74)     0  0    0   0   0   0     0 (0.00)    0   13 (2.46)
40     19   1071    513 ( 32.78)     0  0    0   0   0   0     0 (0.00)    0   13 (2.53)
39     31   1102    494 ( 31.57)     0  0    0   0   0   0     0 (0.00)    0   13 (2.63)
38     22   1124    463 ( 29.58)     0  0    0   0   0   0     0 (0.00)    0   13 (2.81)
37     19   1143    441 ( 28.18)     0  0    0   0   0   0     0 (0.00)    0   13 (2.95)
36      6   1149    422 ( 26.96)     0  0    0   0   0   0     0 (0.00)    0   13 (3.08)
35     19   1168    416 ( 26.58)     0  0    0   0   0   0     0 (0.00)    0   13 (3.12)
34     13   1181    397 ( 25.37)     0  0    0   0   0   0     0 (0.00)    0   13 (3.27)
33     10   1191    384 ( 24.54)     0  0    0   0   0   0     0 (0.00)    0   13 (3.39)
32      7   1198    374 ( 23.90)     0  0    0   0   0   0     0 (0.00)    0   13 (3.48)
31     15   1213    367 ( 23.45)     0  0    0   0   0   0     0 (0.00)    0   13 (3.54)
30      2   1215    352 ( 22.49)     0  0    0   0   0   0     0 (0.00)    0   13 (3.69)
29     24   1239    350 ( 22.36)     0  0    0   0   0   0     0 (0.00)    0   13 (3.71)
28      5   1244    326 ( 20.83)     0  0    0   0   0   0     0 (0.00)    0   13 (3.99)
27     11   1255    321 ( 20.51)     0  0    0   0   0   0     0 (0.00)    0   13 (4.05)
26      1   1256    310 ( 19.81)     0  0    0   0   0   0     0 (0.00)    0   13 (4.19)
25     27   1283    309 ( 19.74)     0  0    0   0   0   0     0 (0.00)    0   13 (4.21)
24      5   1288    282 ( 18.02)     0  0    0   0   0   0     0 (0.00)    0   13 (4.61)
23      6   1294    277 ( 17.70)     0  0    0   0   0   0     0 (0.00)    0   13 (4.69)
22      7   1301    271 ( 17.32)     0  0    0   0   0   0     0 (0.00)    0   13 (4.80)
21     17   1318    264 ( 16.87)     0  0    0   0   0   0     0 (0.00)    0   13 (4.92)
20      8   1326    247 ( 15.78)     0  0    0   0   0   0     0 (0.00)    0   13 (5.26)
19     15   1341    239 ( 15.27)     0  0    0   0   0   0     0 (0.00)    0   13 (5.44)
18      7   1348    224 ( 14.31)     0  0    0   0   0   0     0 (0.00)    0   13 (5.80)
17     11   1359    217 ( 13.87)     0  0    0   0   0   0     0 (0.00)    0   13 (5.99)
16      9   1368    206 ( 13.16)     0  0    0   0   0   0     0 (0.00)    0   13 (6.31)
15     18   1386    197 ( 12.59)     0  0    0   0   0   0     0 (0.00)    0   13 (6.60)
14     12   1398    179 ( 11.44)     0  0    0   0   0   0     0 (0.00)    0   13 (7.26)
13     14   1412    167 ( 10.67)     0  0    0   0   0   0     0 (0.00)    0   13 (7.78)
12     20   1432    153 (  9.78)     0  0    0   1   0   0     1 (5.00)    1   13 (8.50)
11     18   1450    133 (  8.50)     0  0    0   0   0   0     0 (0.00)    1   12 (9.02)
10     37   1487    115 (  7.35)     0  0    0   2   0   0     2 (5.41)    3   12 (10.43)
 9     27   1514     78 (  4.98)     0  0    0   1   0   1     2 (7.41)    5   10 (12.82)
 8     26   1540     51 (  3.26)     0  0    0   4   1   1     6 (23.08)   11    8 (15.69)
 7     14   1554     25 (  1.60)     0  0    0   1   0   0     1 (7.14)   12    2 (8.00)
 6      9   1563     11 (  0.70)     0  0    0   0   0   0     0 (0.00)   12    1 (9.09)
 4      2   1565      2 (  0.13)     0  0    0   1   0   0     1 (50.00)   13    1 (50.00)
-1    342   1907      0 (  0.00)   107  0    0  11   1   7    19 (5.56)   32    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     250      250        2
  6       1      251        3
  7       3      254        5
  8       7      261        6
  9       1      262        6
 10      10      272       11
 11       7      279       12
 12      10      289       15
 13       7      296       14
 14       9      305       18
 15      13      318       17
 16       7      325       15
 17       8      333       16
 18       4      337       16
 19      12      349       17
 20       6      355       14
 21      12      367       11
 22       4      371       12
 23       3      374       12
 24       2      376       12
 25       9      385       13
 26       1      386       13
 27       7      393       13
 28       3      396       13
 29      13      409       14
 30       1      410       14
 31       6      416       14
 32       4      420       16
 33       5      425       16
 34       8      433       15
 35       9      442       14
 36       4      446       13
 37      10      456       11
 38      13      469       14
 39      17      486       17
 40       8      494       18
 41      11      505       17
 42       5      510       16
 43      15      525       16
 44       1      526       16
 45      37      563       24
 46       4      567       24
 47      47      614       37
 48       5      619       36
 49       7      626       34
 50      14      640       30
 51      24      664       35
 52     116      780       37
 53      10      790       39
 54      83      873       40
 55       1      874       40
 56       2      876       38
 57       6      882       37
 60     102      984       23
 66      49     1033        1

SS region: 1033 (100.00%), flagged: 2 (0.19%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality):
   838  S     bg110109f1      (0)/(0)  833 ACCCCAG / AACTCCG
   850  D     bg110109f1      (0)/(0)  844 CCCGCCAT / CGCGGCT
   862  D     bg110109f1      (0)/(0)  857 CGGTTTG / CCGATG
   865  I     bg110109f1      (0)/(0)  865 AC / AAC
   871  D     bg110109f1      (0)/(0)  869 TGCT / TGT
   881  D     bg110109f1      (0)/(0)  879 CGAA / CGA
   891  D     bg110109f1      (0)/(0)  889 GGCA / GGA
   895  S     bg110109f1      (0)/(0)  894 CGC / CCC
    35  S     dg110109f1      (0)/(0)  33 CCGA / CGAA
*   40  D     dg110109f1      (13)/(13)  38 GACT / GAT

0 HQ discrepancies in 0 reads.
10 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 10.  2 reads; 271 bp (untrimmed), 271 (trimmed).
C  -737   318 ae030109r1    247 (  0)  1.48 0.37 0.37  738 (749)   47 ( 47) 
    -19  1026 ae030109f1    242 (  0)  0.00 1.54 0.00   31 ( 31)  755 (755) 

Overall discrep rates (%):             0.75 0.94 0.19

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90     104  38.4     104  38.4    0.00
 89       2   0.7     106  39.1    0.00
 88       2   0.7     108  39.9    0.00
 87       5   1.8     113  41.7    0.00
 86       6   2.2     119  43.9    0.00
 85       7   2.6     126  46.5    0.00
 84       7   2.6     133  49.1    0.00
 83       3   1.1     136  50.2    0.00
 82       3   1.1     139  51.3    0.00
 81       5   1.8     144  53.1    0.00
 80       6   2.2     150  55.4    0.00
 79       1   0.4     151  55.7    0.00
 78       1   0.4     152  56.1    0.00
 77       3   1.1     155  57.2    0.00
 76       3   1.1     158  58.3    0.00
 75       2   0.7     160  59.0    0.00
 74       1   0.4     161  59.4    0.00
 72       1   0.4     162  59.8    0.00
 71      16   5.9     178  65.7    0.00
 66       4   1.5     182  67.2    0.00
 65       6   2.2     188  69.4    0.00
 59       2   0.7     190  70.1    0.00
 58       7   2.6     197  72.7    0.00
 57       8   3.0     205  75.6    0.00
 56      29  10.7     234  86.3    0.00
 51       2   0.7     236  87.1    0.00
 50      13   4.8     249  91.9    0.00
 47       2   0.7     251  92.6    0.00
 46       2   0.7     253  93.4    0.00
 44       3   1.1     256  94.5    0.00
 43       6   2.2     262  96.7    0.00
 42       5   1.8     267  98.5    0.00
 40       2   0.7     269  99.3    0.00
 38       2   0.7     271 100.0    0.00   (quality -1 = terminal quality 0)

Avg. full length: 271.0, trimmed (qual > -1): 271.0
Avg. quality: 74.6 per base

Initial, terminal qual 0 segments:  (None), (None)

Regions of LLR- adjusted quality < 2.0:


1 regions, avg size 0.0, avg spacing 271.0

First_start: 12, last_end: 271

Slack, # used pairs (max_score), unused
 0     1  ( 5.0)     0 ( 0.0)        1

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -    11       11+
  272 - right        0+      ae030109f1   ( -19)    No            290+

Bottom strand: 
 left -     0        0+      ae030109r1   ( 318)    Yes           318+
  272 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56    137    137    535 (100.00)     0  0    0   0   0   0     0 (0.00)    0   10 (1.87)
51     22    159    398 ( 74.39)     0  0    0   0   0   0     0 (0.00)    0   10 (2.51)
50     51    210    376 ( 70.28)     0  0    0   0   0   0     0 (0.00)    0   10 (2.66)
48      3    213    325 ( 60.75)     0  0    0   0   0   0     0 (0.00)    0   10 (3.08)
47      3    216    322 ( 60.19)     0  0    0   0   0   0     0 (0.00)    0   10 (3.11)
46      8    224    319 ( 59.63)     0  0    0   0   0   0     0 (0.00)    0   10 (3.13)
45      3    227    311 ( 58.13)     0  0    0   0   0   0     0 (0.00)    0   10 (3.22)
44     26    253    308 ( 57.57)     0  0    0   0   0   0     0 (0.00)    0   10 (3.25)
43     29    282    282 ( 52.71)     0  0    0   0   0   0     0 (0.00)    0   10 (3.55)
42     65    347    253 ( 47.29)     0  0    0   0   0   0     0 (0.00)    0   10 (3.95)
41      4    351    188 ( 35.14)     0  0    0   0   0   0     0 (0.00)    0   10 (5.32)
40     46    397    184 ( 34.39)     0  0    0   0   0   0     0 (0.00)    0   10 (5.43)
39      1    398    138 ( 25.79)     0  0    0   0   0   0     0 (0.00)    0   10 (7.25)
38      2    400    137 ( 25.61)     0  0    0   0   0   0     0 (0.00)    0   10 (7.30)
37     15    415    135 ( 25.23)     0  0    0   0   0   0     0 (0.00)    0   10 (7.41)
35      5    420    120 ( 22.43)     0  0    0   0   0   0     0 (0.00)    0   10 (8.33)
34      5    425    115 ( 21.50)     0  0    0   0   0   0     0 (0.00)    0   10 (8.70)
33      8    433    110 ( 20.56)     0  0    0   0   0   0     0 (0.00)    0   10 (9.09)
32     10    443    102 ( 19.07)     0  0    0   0   0   0     0 (0.00)    0   10 (9.80)
31      3    446     92 ( 17.20)     0  0    0   0   0   0     0 (0.00)    0   10 (10.87)
30      2    448     89 ( 16.64)     0  0    0   0   0   0     0 (0.00)    0   10 (11.24)
29     14    462     87 ( 16.26)     0  0    0   0   0   0     0 (0.00)    0   10 (11.49)
28      2    464     73 ( 13.64)     0  0    0   0   0   0     0 (0.00)    0   10 (13.70)
27      6    470     71 ( 13.27)     0  0    0   0   0   0     0 (0.00)    0   10 (14.08)
25      1    471     65 ( 12.15)     0  0    0   0   0   0     0 (0.00)    0   10 (15.38)
24      3    474     64 ( 11.96)     0  0    0   0   0   0     0 (0.00)    0   10 (15.62)
23      4    478     61 ( 11.40)     0  0    0   0   0   0     0 (0.00)    0   10 (16.39)
22      1    479     57 ( 10.65)     0  0    0   0   0   0     0 (0.00)    0   10 (17.54)
20      1    480     56 ( 10.47)     0  0    0   0   0   0     0 (0.00)    0   10 (17.86)
19      6    486     55 ( 10.28)     0  0    0   0   0   0     0 (0.00)    0   10 (18.18)
18      1    487     49 (  9.16)     0  0    0   0   0   0     0 (0.00)    0   10 (20.41)
16      3    490     48 (  8.97)     0  0    0   0   0   0     0 (0.00)    0   10 (20.83)
15      4    494     45 (  8.41)     0  0    0   0   0   0     0 (0.00)    0   10 (22.22)
14      2    496     41 (  7.66)     0  0    0   0   0   0     0 (0.00)    0   10 (24.39)
13      6    502     39 (  7.29)     0  0    0   0   0   0     0 (0.00)    0   10 (25.64)
12      3    505     33 (  6.17)     0  0    0   0   0   0     0 (0.00)    0   10 (30.30)
11      2    507     30 (  5.61)     0  0    0   0   0   0     0 (0.00)    0   10 (33.33)
10      2    509     28 (  5.23)     0  0    0   0   0   0     0 (0.00)    0   10 (35.71)
 9      7    516     26 (  4.86)     0  0    0   1   0   0     1 (14.29)    1   10 (38.46)
 8      5    521     19 (  3.55)     0  0    0   3   0   1     4 (80.00)    5    9 (47.37)
 7      4    525     14 (  2.62)     0  0    0   0   2   0     2 (50.00)    7    5 (35.71)
 6      3    528     10 (  1.87)     0  0    0   0   1   0     1 (33.33)    8    3 (30.00)
 4      6    534      7 (  1.31)     0  0    0   0   1   0     1 (16.67)    9    2 (28.57)
 0      1    535      1 (  0.19)     0  0    0   0   1   0     1 (100.00)   10    1 (100.00)
-1      0    535      0 (  0.00)    11  0    0   0   0   0     0 (0.00)   10    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90    208    208    535 (100.00)     0  0    0   0   0   0     0 (0.00)    0   10 (1.87)
89      4    212    327 ( 61.12)     0  0    0   0   0   0     0 (0.00)    0   10 (3.06)
88      3    215    323 ( 60.37)     0  0    0   0   0   0     0 (0.00)    0   10 (3.10)
87     10    225    320 ( 59.81)     0  0    0   0   0   0     0 (0.00)    0   10 (3.12)
86     12    237    310 ( 57.94)     0  0    0   0   0   0     0 (0.00)    0   10 (3.23)
85     14    251    298 ( 55.70)     0  0    0   0   0   0     0 (0.00)    0   10 (3.36)
84     14    265    284 ( 53.08)     0  0    0   0   0   0     0 (0.00)    0   10 (3.52)
83      6    271    270 ( 50.47)     0  0    0   0   0   0     0 (0.00)    0   10 (3.70)
82      6    277    264 ( 49.35)     0  0    0   0   0   0     0 (0.00)    0   10 (3.79)
81     10    287    258 ( 48.22)     0  0    0   0   0   0     0 (0.00)    0   10 (3.88)
80     12    299    248 ( 46.36)     0  0    0   0   0   0     0 (0.00)    0   10 (4.03)
79      2    301    236 ( 44.11)     0  0    0   0   0   0     0 (0.00)    0   10 (4.24)
78      2    303    234 ( 43.74)     0  0    0   0   0   0     0 (0.00)    0   10 (4.27)
77      6    309    232 ( 43.36)     0  0    0   0   0   0     0 (0.00)    0   10 (4.31)
76      6    315    226 ( 42.24)     0  0    0   0   0   0     0 (0.00)    0   10 (4.42)
75      4    319    220 ( 41.12)     0  0    0   0   0   0     0 (0.00)    0   10 (4.55)
74      2    321    216 ( 40.37)     0  0    0   0   0   0     0 (0.00)    0   10 (4.63)
72      2    323    214 ( 40.00)     0  0    0   0   0   0     0 (0.00)    0   10 (4.67)
71     17    340    212 ( 39.63)     0  0    0   0   0   0     0 (0.00)    0   10 (4.72)
66      4    344    195 ( 36.45)     0  0    0   0   0   0     0 (0.00)    0   10 (5.13)
65      6    350    191 ( 35.70)     0  0    0   0   0   0     0 (0.00)    0   10 (5.24)
63      1    351    185 ( 34.58)     0  0    0   0   0   0     0 (0.00)    0   10 (5.41)
59      2    353    184 ( 34.39)     0  0    0   0   0   0     0 (0.00)    0   10 (5.43)
58      7    360    182 ( 34.02)     0  0    0   0   0   0     0 (0.00)    0   10 (5.49)
57      8    368    175 ( 32.71)     0  0    0   0   0   0     0 (0.00)    0   10 (5.71)
56     30    398    167 ( 31.21)     0  0    0   0   0   0     0 (0.00)    0   10 (5.99)
55     11    409    137 ( 25.61)     0  0    0   0   0   0     0 (0.00)    0   10 (7.30)
51      2    411    126 ( 23.55)     0  0    0   0   0   0     0 (0.00)    0   10 (7.94)
50     13    424    124 ( 23.18)     0  0    0   0   0   0     0 (0.00)    0   10 (8.06)
47      9    433    111 ( 20.75)     0  0    0   0   0   0     0 (0.00)    0   10 (9.01)
46      2    435    102 ( 19.07)     0  0    0   0   0   0     0 (0.00)    0   10 (9.80)
45      2    437    100 ( 18.69)     0  0    0   0   0   0     0 (0.00)    0   10 (10.00)
44     13    450     98 ( 18.32)     0  0    0   0   0   0     0 (0.00)    0   10 (10.20)
43      6    456     85 ( 15.89)     0  0    0   0   0   0     0 (0.00)    0   10 (11.76)
42      9    465     79 ( 14.77)     0  0    0   0   0   0     0 (0.00)    0   10 (12.66)
40      3    468     70 ( 13.08)     0  0    0   0   0   0     0 (0.00)    0   10 (14.29)
39      1    469     67 ( 12.52)     0  0    0   0   0   0     0 (0.00)    0   10 (14.93)
38      6    475     66 ( 12.34)     0  0    0   0   0   0     0 (0.00)    0   10 (15.15)
37      1    476     60 ( 11.21)     0  0    0   0   0   0     0 (0.00)    0   10 (16.67)
35      1    477     59 ( 11.03)     0  0    0   0   0   0     0 (0.00)    0   10 (16.95)
34      4    481     58 ( 10.84)     0  0    0   0   0   0     0 (0.00)    0   10 (17.24)
32      1    482     54 ( 10.09)     0  0    0   0   0   0     0 (0.00)    0   10 (18.52)
31      2    484     53 (  9.91)     0  0    0   0   0   0     0 (0.00)    0   10 (18.87)
29      1    485     51 (  9.53)     0  0    0   0   0   0     0 (0.00)    0   10 (19.61)
28      1    486     50 (  9.35)     0  0    0   0   0   0     0 (0.00)    0   10 (20.00)
27      1    487     49 (  9.16)     0  0    0   0   0   0     0 (0.00)    0   10 (20.41)
24      3    490     48 (  8.97)     0  0    0   0   0   0     0 (0.00)    0   10 (20.83)
23      1    491     45 (  8.41)     0  0    0   0   0   0     0 (0.00)    0   10 (22.22)
20      1    492     44 (  8.22)     0  0    0   0   0   0     0 (0.00)    0   10 (22.73)
19      2    494     43 (  8.04)     0  0    0   0   0   0     0 (0.00)    0   10 (23.26)
18      1    495     41 (  7.66)     0  0    0   0   0   0     0 (0.00)    0   10 (24.39)
16      1    496     40 (  7.48)     0  0    0   0   0   0     0 (0.00)    0   10 (25.00)
15      4    500     39 (  7.29)     0  0    0   0   0   0     0 (0.00)    0   10 (25.64)
14      1    501     35 (  6.54)     0  0    0   0   0   0     0 (0.00)    0   10 (28.57)
13      5    506     34 (  6.36)     0  0    0   0   0   0     0 (0.00)    0   10 (29.41)
12      2    508     29 (  5.42)     0  0    0   0   0   0     0 (0.00)    0   10 (34.48)
11      2    510     27 (  5.05)     0  0    0   0   0   0     0 (0.00)    0   10 (37.04)
10      2    512     25 (  4.67)     0  0    0   0   0   0     0 (0.00)    0   10 (40.00)
 9      5    517     23 (  4.30)     0  0    0   1   0   0     1 (20.00)    1   10 (43.48)
 8      4    521     18 (  3.36)     0  0    0   3   0   1     4 (100.00)    5    9 (50.00)
 7      4    525     14 (  2.62)     0  0    0   0   2   0     2 (50.00)    7    5 (35.71)
 6      3    528     10 (  1.87)     0  0    0   0   1   0     1 (33.33)    8    3 (30.00)
 4      6    534      7 (  1.31)     0  0    0   0   1   0     1 (16.67)    9    2 (28.57)
 0      1    535      1 (  0.19)     0  0    0   0   1   0     1 (100.00)   10    1 (100.00)
-1      0    535      0 (  0.00)    11  0    0   0   0   0     0 (0.00)   10    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
 38       2        2        2
 40       2        4        2
 42       5        9        5
 43       6       15        5
 44       3       18        6
 46       2       20        5
 47       2       22        7
 50      13       35        7
 51       2       37        7
 56      29       66        8
 57       8       74       11
 58       7       81       12
 59       2       83       11
 65       6       89       10
 66       4       93       11
 71      16      109        8
 72       1      110        7
 74       1      111        7
 75       2      113        8
 76       3      116       10
 77       3      119       11
 78       1      120       12
 79       1      121       13
 80       6      127       14
 81       5      132       14
 82       3      135       13
 83       3      138       13
 84       7      145       14
 85       7      152       14
 86       6      158       15
 87       5      163       14
 88       2      165       13
 89       2      167       13
 90     104      271        1

SS region: 11 (4.06%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
  271     -3.2  [-3.2,  0.0]  (0, 1)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 11.  2 reads; 1049 bp (untrimmed), 872 (trimmed).  Isolated contig.
      1  1041 be070109f1    903 (  0)  1.37 1.56 0.29    0 ( 19)   16 (161) 
     -1  1049 cg060109f1   1004 (  0)  0.58 0.00 0.29   12 ( 20)    0 (157) 

Overall discrep rates (%):             0.97 0.78 0.29

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 66     386  36.8     386  36.8    0.00
 61      73   7.0     459  43.8    0.00
 60       5   0.5     464  44.2    0.00
 58       1   0.1     465  44.3    0.00
 57       1   0.1     466  44.4    0.00
 56      16   1.5     482  45.9    0.00
 55      11   1.0     493  47.0    0.00
 54      10   1.0     503  48.0    0.00
 53      22   2.1     525  50.0    0.00
 52      33   3.1     558  53.2    0.00
 51      10   1.0     568  54.1    0.00
 50      30   2.9     598  57.0    0.00
 48       5   0.5     603  57.5    0.00
 47      17   1.6     620  59.1    0.00
 46       1   0.1     621  59.2    0.00
 45      22   2.1     643  61.3    0.00
 44       5   0.5     648  61.8    0.00
 43      15   1.4     663  63.2    0.00
 42       7   0.7     670  63.9    0.00
 41       5   0.5     675  64.3    0.00
 40       1   0.1     676  64.4    0.00
 39       6   0.6     682  65.0    0.00
 38       7   0.7     689  65.7    0.01
 37       3   0.3     692  66.0    0.01
 36       3   0.3     695  66.3    0.01
 35      11   1.0     706  67.3    0.01
 34       2   0.2     708  67.5    0.01
 33       8   0.8     716  68.3    0.02
 32       5   0.5     721  68.7    0.02
 31       9   0.9     730  69.6    0.03
 30       3   0.3     733  69.9    0.03
 29      11   1.0     744  70.9    0.04
 28       6   0.6     750  71.5    0.05
 27       8   0.8     758  72.3    0.07
 26       3   0.3     761  72.5    0.08
 25       9   0.9     770  73.4    0.10
 24       6   0.6     776  74.0    0.13
 23       1   0.1     777  74.1    0.13
 22       4   0.4     781  74.5    0.16
 21       3   0.3     784  74.7    0.18
 20       4   0.4     788  75.1    0.22
 19       8   0.8     796  75.9    0.32
 18       4   0.4     800  76.3    0.39
 17       6   0.6     806  76.8    0.51
 16       3   0.3     809  77.1    0.58
 15      13   1.2     822  78.4    0.99
 14       5   0.5     827  78.8    1.19
 13       5   0.5     832  79.3    1.44
 12       7   0.7     839  80.0    1.88
 11      12   1.1     851  81.1    2.84
 10       8   0.8     859  81.9    3.64
  9       5   0.5     864  82.4    4.27
  8       1   0.1     865  82.5    4.42
  7       7   0.7     872  83.1    5.82
 -1     177  16.9    1049 100.0  182.82   (quality -1 = terminal quality 0)

Avg. full length: 1049.0, trimmed (qual > -1): 872.0
Avg. quality: 43.1 per base

Initial, terminal qual 0 segments:  1-19, 892-1049

Regions of LLR- adjusted quality < 2.0:
1-21, 25, 78-85, 751-755, 765, 793-794, 796-807, 815-817, 
819-820, 824-827, 835-838, 841-843, 852-876, 880-1049, 

14 regions, avg size 18.6, avg spacing 74.9

First_start: 19, last_end: 892

Slack, # used pairs (max_score), unused
 0     0  ( 0.0)     0 ( 0.0)        1
 2     1  (21.5)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 1050 - right        0+      be070109f1   (   1)    No           1048+

Bottom strand: 
 left - right     1049+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56    599    599   2040 (100.00)     0  0    0   0   0   0     0 (0.00)    0   40 (1.96)
51    180    779   1441 ( 70.64)     0  0    0   0   0   0     0 (0.00)    0   40 (2.78)
50     22    801   1261 ( 61.81)     0  0    0   0   0   0     0 (0.00)    0   40 (3.17)
48      2    803   1239 ( 60.74)     0  0    0   0   0   0     0 (0.00)    0   40 (3.23)
47      4    807   1237 ( 60.64)     0  0    0   0   0   0     0 (0.00)    0   40 (3.23)
46     30    837   1233 ( 60.44)     0  0    0   0   0   0     0 (0.00)    0   40 (3.24)
45     25    862   1203 ( 58.97)     0  0    0   0   0   0     0 (0.00)    0   40 (3.33)
44     19    881   1178 ( 57.75)     0  0    0   0   0   0     0 (0.00)    0   40 (3.40)
43     70    951   1159 ( 56.81)     0  0    0   0   0   0     0 (0.00)    0   40 (3.45)
42     73   1024   1089 ( 53.38)     0  0    0   0   0   0     0 (0.00)    0   40 (3.67)
41     25   1049   1016 ( 49.80)     0  0    0   0   0   0     0 (0.00)    0   40 (3.94)
40     80   1129    991 ( 48.58)     0  0    0   0   0   0     0 (0.00)    0   40 (4.04)
38      6   1135    911 ( 44.66)     0  0    0   0   0   0     0 (0.00)    0   40 (4.39)
37     28   1163    905 ( 44.36)     0  0    0   0   0   0     0 (0.00)    0   40 (4.42)
36      1   1164    877 ( 42.99)     0  0    0   0   0   0     0 (0.00)    0   40 (4.56)
35     42   1206    876 ( 42.94)     0  0    0   0   0   0     0 (0.00)    0   40 (4.57)
34     20   1226    834 ( 40.88)     0  0    0   0   0   0     0 (0.00)    0   40 (4.80)
33     26   1252    814 ( 39.90)     0  0    0   0   0   0     0 (0.00)    0   40 (4.91)
32     16   1268    788 ( 38.63)     0  0    0   0   0   0     0 (0.00)    0   40 (5.08)
31     18   1286    772 ( 37.84)     0  0    0   0   0   0     0 (0.00)    0   40 (5.18)
30      8   1294    754 ( 36.96)     0  0    0   0   0   0     0 (0.00)    0   40 (5.31)
29     28   1322    746 ( 36.57)     0  0    0   0   0   0     0 (0.00)    0   40 (5.36)
28     12   1334    718 ( 35.20)     0  0    0   0   0   0     0 (0.00)    0   40 (5.57)
27     19   1353    706 ( 34.61)     0  0    0   0   0   0     0 (0.00)    0   40 (5.67)
26      9   1362    687 ( 33.68)     0  0    0   0   0   0     0 (0.00)    0   40 (5.82)
25     21   1383    678 ( 33.24)     0  0    0   0   0   0     0 (0.00)    0   40 (5.90)
24     16   1399    657 ( 32.21)     0  0    0   0   0   0     0 (0.00)    0   40 (6.09)
23     18   1417    641 ( 31.42)     0  0    0   0   0   0     0 (0.00)    0   40 (6.24)
22      8   1425    623 ( 30.54)     0  0    0   0   0   0     0 (0.00)    0   40 (6.42)
21     21   1446    615 ( 30.15)     0  0    0   0   0   0     0 (0.00)    0   40 (6.50)
20     12   1458    594 ( 29.12)     0  0    0   0   0   0     0 (0.00)    0   40 (6.73)
19     22   1480    582 ( 28.53)     0  0    0   0   0   0     0 (0.00)    0   40 (6.87)
18     14   1494    560 ( 27.45)     0  0    0   0   0   0     0 (0.00)    0   40 (7.14)
17     24   1518    546 ( 26.76)     0  0    0   0   0   0     0 (0.00)    0   40 (7.33)
16     22   1540    522 ( 25.59)     0  0    0   1   0   0     1 (4.55)    1   40 (7.66)
15     26   1566    500 ( 24.51)     0  0    0   2   0   0     2 (7.69)    3   39 (7.80)
14     22   1588    474 ( 23.24)     0  0    0   0   0   1     1 (4.55)    4   37 (7.81)
13     22   1610    452 ( 22.16)     0  0    0   1   0   0     1 (4.55)    5   36 (7.96)
12     27   1637    430 ( 21.08)     0  0    0   0   0   0     0 (0.00)    5   35 (8.14)
11     49   1686    403 ( 19.75)     0  0    0   1   0   0     1 (2.04)    6   35 (8.68)
10     64   1750    354 ( 17.35)     0  0    0   4   1   2     7 (10.94)   13   34 (9.60)
 9     82   1832    290 ( 14.22)     0  0    0   1   2   1     4 (4.88)   17   27 (9.31)
 8     85   1917    208 ( 10.20)     0  0    0   3   6   1    10 (11.76)   27   23 (11.06)
 7     90   2007    123 (  6.03)     0  0    0   5   3   1     9 (10.00)   36   13 (10.57)
 6     33   2040     33 (  1.62)     0  0    0   2   2   0     4 (12.12)   40    4 (12.12)
-1     34   2074      0 (  0.00)    26  0    0   0   0   0     0 (0.00)   40    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
66    772    772   1745 (100.00)     0  0    0   0   0   0     0 (0.00)    0   16 (0.92)
61    144    916    973 ( 55.76)     0  0    0   0   0   0     0 (0.00)    0   16 (1.64)
60     10    926    829 ( 47.51)     0  0    0   0   0   0     0 (0.00)    0   16 (1.93)
58      2    928    819 ( 46.93)     0  0    0   0   0   0     0 (0.00)    0   16 (1.95)
57      2    930    817 ( 46.82)     0  0    0   0   0   0     0 (0.00)    0   16 (1.96)
56     31    961    815 ( 46.70)     0  0    0   0   0   0     0 (0.00)    0   16 (1.96)
55     22    983    784 ( 44.93)     0  0    0   0   0   0     0 (0.00)    0   16 (2.04)
54     20   1003    762 ( 43.67)     0  0    0   0   0   0     0 (0.00)    0   16 (2.10)
53     42   1045    742 ( 42.52)     0  0    0   0   0   0     0 (0.00)    0   16 (2.16)
52     68   1113    700 ( 40.11)     0  0    0   0   0   0     0 (0.00)    0   16 (2.29)
51     16   1129    632 ( 36.22)     0  0    0   0   0   0     0 (0.00)    0   16 (2.53)
50     59   1188    616 ( 35.30)     0  0    0   0   0   0     0 (0.00)    0   16 (2.60)
48     10   1198    557 ( 31.92)     0  0    0   0   0   0     0 (0.00)    0   16 (2.87)
47     34   1232    547 ( 31.35)     0  0    0   0   0   0     0 (0.00)    0   16 (2.93)
46      1   1233    513 ( 29.40)     0  0    0   0   0   0     0 (0.00)    0   16 (3.12)
45     44   1277    512 ( 29.34)     0  0    0   0   0   0     0 (0.00)    0   16 (3.12)
44     11   1288    468 ( 26.82)     0  0    0   0   0   0     0 (0.00)    0   16 (3.42)
43     28   1316    457 ( 26.19)     0  0    0   0   0   0     0 (0.00)    0   16 (3.50)
42     12   1328    429 ( 24.58)     0  0    0   0   0   0     0 (0.00)    0   16 (3.73)
41     12   1340    417 ( 23.90)     0  0    0   0   0   0     0 (0.00)    0   16 (3.84)
40      2   1342    405 ( 23.21)     0  0    0   0   0   0     0 (0.00)    0   16 (3.95)
39     11   1353    403 ( 23.09)     0  0    0   0   0   0     0 (0.00)    0   16 (3.97)
38     10   1363    392 ( 22.46)     0  0    0   0   0   0     0 (0.00)    0   16 (4.08)
37      5   1368    382 ( 21.89)     0  0    0   0   0   0     0 (0.00)    0   16 (4.19)
36      5   1373    377 ( 21.60)     0  0    0   0   0   0     0 (0.00)    0   16 (4.24)
35     22   1395    372 ( 21.32)     0  0    0   0   0   0     0 (0.00)    0   16 (4.30)
34      5   1400    350 ( 20.06)     0  0    0   0   0   0     0 (0.00)    0   16 (4.57)
33     13   1413    345 ( 19.77)     0  0    0   0   0   0     0 (0.00)    0   16 (4.64)
32      7   1420    332 ( 19.03)     0  0    0   0   0   0     0 (0.00)    0   16 (4.82)
31     13   1433    325 ( 18.62)     0  0    0   0   0   0     0 (0.00)    0   16 (4.92)
30      4   1437    312 ( 17.88)     0  0    0   0   0   0     0 (0.00)    0   16 (5.13)
29     17   1454    308 ( 17.65)     0  0    0   0   0   0     0 (0.00)    0   16 (5.19)
28     11   1465    291 ( 16.68)     0  0    0   0   0   0     0 (0.00)    0   16 (5.50)
27     13   1478    280 ( 16.05)     0  0    0   0   0   0     0 (0.00)    0   16 (5.71)
26      5   1483    267 ( 15.30)     0  0    0   0   0   0     0 (0.00)    0   16 (5.99)
25     11   1494    262 ( 15.01)     0  0    0   0   0   0     0 (0.00)    0   16 (6.11)
24     12   1506    251 ( 14.38)     0  0    0   0   0   0     0 (0.00)    0   16 (6.37)
23      3   1509    239 ( 13.70)     0  0    0   0   0   0     0 (0.00)    0   16 (6.69)
22      4   1513    236 ( 13.52)     0  0    0   0   0   0     0 (0.00)    0   16 (6.78)
21      8   1521    232 ( 13.30)     0  0    0   0   0   0     0 (0.00)    0   16 (6.90)
20      7   1528    224 ( 12.84)     0  0    0   0   0   0     0 (0.00)    0   16 (7.14)
19     15   1543    217 ( 12.44)     0  0    0   0   0   0     0 (0.00)    0   16 (7.37)
18      9   1552    202 ( 11.58)     0  0    0   0   0   0     0 (0.00)    0   16 (7.92)
17     12   1564    193 ( 11.06)     0  0    0   0   0   0     0 (0.00)    0   16 (8.29)
16      8   1572    181 ( 10.37)     0  0    0   0   0   0     0 (0.00)    0   16 (8.84)
15     24   1596    173 (  9.91)     0  0    0   2   0   0     2 (8.33)    2   16 (9.25)
14      8   1604    149 (  8.54)     0  0    0   0   0   1     1 (12.50)    3   14 (9.40)
13     12   1616    141 (  8.08)     0  0    0   0   0   0     0 (0.00)    3   13 (9.22)
12     13   1629    129 (  7.39)     0  0    0   0   0   0     0 (0.00)    3   13 (10.08)
11     19   1648    116 (  6.65)     0  0    0   0   0   0     0 (0.00)    3   13 (11.21)
10     29   1677     97 (  5.56)     0  0    0   2   1   1     4 (13.79)    7   13 (13.40)
 9     20   1697     68 (  3.90)     0  0    0   0   0   1     1 (5.00)    8    9 (13.24)
 8     15   1712     48 (  2.75)     0  0    0   1   2   0     3 (20.00)   11    8 (16.67)
 7     28   1740     33 (  1.89)     0  0    0   2   0   1     3 (10.71)   14    5 (15.15)
 6      5   1745      5 (  0.29)     0  0    0   1   1   0     2 (40.00)   16    2 (40.00)
-1    329   2074      0 (  0.00)    26  0    0  12  10   2    24 (7.29)   40    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     177      177        2
  7       7      184        6
  8       1      185        6
  9       5      190        6
 10       8      198       11
 11      12      210        9
 12       7      217       10
 13       5      222       12
 14       5      227       10
 15      13      240       15
 16       3      243       17
 17       6      249       19
 18       4      253       19
 19       8      261       14
 20       4      265       13
 21       3      268       13
 22       4      272       12
 23       1      273       12
 24       6      279       10
 25       9      288       10
 26       3      291       11
 27       8      299       13
 28       6      305       12
 29      11      316       15
 30       3      319       15
 31       9      328       14
 32       5      333       14
 33       8      341       12
 34       2      343       11
 35      11      354       10
 36       3      357        9
 37       3      360        9
 38       7      367       10
 39       6      373        9
 40       1      374        9
 41       5      379        8
 42       7      386       10
 43      15      401       15
 44       5      406       18
 45      22      428       21
 46       1      429       21
 47      17      446       22
 48       5      451       21
 50      30      481       14
 51      10      491       17
 52      33      524       22
 53      22      546       26
 54      10      556       25
 55      11      567       26
 56      16      583       27
 57       1      584       26
 58       1      585       25
 60       5      590       27
 61      73      663       31
 66     386     1049        1

SS region: 1049 (100.00%), flagged: 4 (0.38%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality):
   896  D     be070109f1      (0)/(0)  894 GAGT / GAT
   900  S     be070109f1      (0)/(0)  899 TCC / TAC
   904  I     be070109f1      (0)/(0)  904 AT / AAT
   913  I     be070109f1      (0)/(0)  909 AATGGT / ATTTGTT
   923  I     be070109f1      (0)/(0)  923 AC / AAC
   931  I     be070109f1      (0)/(0)  931 GC / GGC
   957  S     be070109f1      (0)/(0)  954 TATTA / TTATAA
   966  I     be070109f1      (0)/(0)  964 GCGT / GGGCTT
   970  S     be070109f1      (0)/(0)  969 AAA / AGA
   977  S     be070109f1      (0)/(0)  976 GGA / GAA
   981  S     be070109f1      (0)/(0)  980 AGG / AAG
  1001  I     be070109f1      (0)/(0)  993 CCTCGTCCAG / CTTCCTTCATG
  1007  I     be070109f1      (0)/(0)  1007 GA / GGA
  1012  I     be070109f1      (0)/(0)  1012 TA / TAA
   936  D     cg060109f1      (0)/(0)  934 TGGC / TGC

0 HQ discrepancies in 0 reads.
15 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 12.  3 reads; 51 bp (untrimmed), 0 (trimmed).  Isolated contig.
      1  1056 df060109r1     50 (  0)  0.00 0.00 0.00    0 ( 14) 1005 (1005) 
      1  1047 cf100109r1     28 (  0)  2.33 0.00 4.65    8 (  9)  996 (996) 
      4  1009 dh110109r1     31 (  0)  0.00 0.00 2.70   11 (  7)  958 (958) 

Overall discrep rates (%):             0.76 0.00 2.29

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 -1      51 100.0      51 100.0   51.00   (quality -1 = terminal quality 0)

Avg. full length: 51.0, trimmed (qual > -1): 0.0
Avg. quality: 0.0 per base

Initial, terminal qual 0 segments:  1-51, (None)

Regions of LLR- adjusted quality < 2.0:
1-51, 

1 regions, avg size 51.0, avg spacing 51.0

First_start: 11, last_end: 51

Slack, # used pairs (max_score), unused
 0     2  ( 0.0)     0 ( 0.0)        2

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
   52 - right        0+      dh110109r1   (   4)    No             47+

Bottom strand: 
 left - right       51+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
48      2      2    113 (100.00)     0  0    0   0   0   0     0 (0.00)    0    4 (3.54)
44      2      4    111 ( 98.23)     0  0    0   0   0   0     0 (0.00)    0    4 (3.60)
40      6     10    109 ( 96.46)     0  0    0   0   0   0     0 (0.00)    0    4 (3.67)
33      1     11    103 ( 91.15)     0  0    0   0   0   0     0 (0.00)    0    4 (3.88)
32      1     12    102 ( 90.27)     0  0    0   0   0   0     0 (0.00)    0    4 (3.92)
30      1     13    101 ( 89.38)     0  0    0   0   0   0     0 (0.00)    0    4 (3.96)
29      3     16    100 ( 88.50)     0  0    0   0   0   0     0 (0.00)    0    4 (4.00)
28      1     17     97 ( 85.84)     0  0    0   0   0   0     0 (0.00)    0    4 (4.12)
27      4     21     96 ( 84.96)     0  0    0   0   0   0     0 (0.00)    0    4 (4.17)
26      3     24     92 ( 81.42)     0  0    0   0   0   0     0 (0.00)    0    4 (4.35)
25      4     28     89 ( 78.76)     0  0    0   0   0   1     1 (25.00)    1    4 (4.49)
23      1     29     85 ( 75.22)     0  0    0   0   0   0     0 (0.00)    1    3 (3.53)
22      1     30     84 ( 74.34)     0  0    0   0   0   0     0 (0.00)    1    3 (3.57)
21      1     31     83 ( 73.45)     0  0    0   0   0   0     0 (0.00)    1    3 (3.61)
20      3     34     82 ( 72.57)     0  0    0   0   0   0     0 (0.00)    1    3 (3.66)
19      1     35     79 ( 69.91)     0  0    0   0   0   0     0 (0.00)    1    3 (3.80)
17      8     43     78 ( 69.03)     0  0    0   0   0   1     1 (12.50)    2    3 (3.85)
16      4     47     70 ( 61.95)     0  0    0   0   0   0     0 (0.00)    2    2 (2.86)
15      2     49     66 ( 58.41)     0  0    0   0   0   0     0 (0.00)    2    2 (3.03)
14      3     52     64 ( 56.64)     0  0    0   0   0   0     0 (0.00)    2    2 (3.12)
13     13     65     61 ( 53.98)     0  0    0   0   0   0     0 (0.00)    2    2 (3.28)
12      1     66     48 ( 42.48)     0  0    0   0   0   0     0 (0.00)    2    2 (4.17)
11      5     71     47 ( 41.59)     1  0    0   0   0   1     1 (20.00)    3    2 (4.26)
10      8     79     42 ( 37.17)     1  0    0   0   0   0     0 (0.00)    3    1 (2.38)
 9     15     94     34 ( 30.09)     0  0    0   0   0   0     0 (0.00)    3    1 (2.94)
 8     10    104     19 ( 16.81)     2  0    0   1   0   0     1 (10.00)    4    1 (5.26)
 7      5    109      9 (  7.96)     0  0    0   0   0   0     0 (0.00)    4    0 (0.00)
 6      4    113      4 (  3.54)     0  0    0   0   0   0     0 (0.00)    4    0 (0.00)
-1     15    128      0 (  0.00)    15  0    0   0   0   0     0 (0.00)    4    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
-1    128    128      0 (  0.00)    19  0    0   1   0   3     4 (3.12)    4    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      51       51        1

SS region: 51 (100.00%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
   34     -4.2  [-2.5,  0.0]  (2, 0)

Read/contig discrepancies (* = higher-quality):
    14  D     cf100109r1      (0)/(0)  12 CGTC / CGC
    25  S     cf100109r1      (0)/(0)  24 GCC / GGC
    34  D     cf100109r1      (0)/(0)  32 AGTA / AGA
    34  D     dh110109r1      (0)/(0)  32 AGTA / AGA

0 HQ discrepancies in 0 reads.
4 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 13.  4 reads; 235 bp (untrimmed), 235 (trimmed).
C  -713   283 eg080109r1    216 (  0)  1.70 0.00 0.00  714 (714)   48 ( 48) 
C  -665   284 eg110109r1    218 (  0)  1.28 0.00 0.00  666 (666)   49 ( 49) 
    -12   946 eg110109f1    220 ( 49)  0.00 0.43 0.00   16 ( 16)  711 (711) 
     -8   984 eg080109f1    217 ( 49)  0.86 0.00 0.00   12 ( 16)  749 (749) 

Overall discrep rates (%):             0.96 0.11 0.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90     187  79.6     187  79.6    0.00
 89       3   1.3     190  80.9    0.00
 87       4   1.7     194  82.6    0.00
 86       3   1.3     197  83.8    0.00
 85       3   1.3     200  85.1    0.00
 84       3   1.3     203  86.4    0.00
 81      11   4.7     214  91.1    0.00
 67       2   0.9     216  91.9    0.00
 66       5   2.1     221  94.0    0.00
 61       2   0.9     223  94.9    0.00
 60       5   2.1     228  97.0    0.00
 56       2   0.9     230  97.9    0.00
 55       2   0.9     232  98.7    0.00
 46       1   0.4     233  99.1    0.00
 44       1   0.4     234  99.6    0.00
 43       1   0.4     235 100.0    0.00   (quality -1 = terminal quality 0)

Avg. full length: 235.0, trimmed (qual > -1): 235.0
Avg. quality: 86.6 per base

Initial, terminal qual 0 segments:  (None), (None)

Regions of LLR- adjusted quality < 2.0:


1 regions, avg size 0.0, avg spacing 235.0

First_start: 1, last_end: 235

Slack, # used pairs (max_score), unused
 0     6  ( 5.2)     0 ( 0.0)        6

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     3        3+
  236 - right        0+      eg080109f1   (  -8)    No            243+

Bottom strand: 
 left -     0        0+      eg080109r1   ( 283)    Yes           283+
  236 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56    265    265    935 (100.00)     0  0    0   0   0   0     0 (0.00)    0   10 (1.07)
51     50    315    670 ( 71.66)     0  0    0   0   0   0     0 (0.00)    0   10 (1.49)
50     29    344    620 ( 66.31)     0  0    0   0   0   0     0 (0.00)    0   10 (1.61)
48      2    346    591 ( 63.21)     0  0    0   0   0   0     0 (0.00)    0   10 (1.69)
47      8    354    589 ( 62.99)     0  0    0   0   0   0     0 (0.00)    0   10 (1.70)
46     31    385    581 ( 62.14)     0  0    0   0   0   0     0 (0.00)    0   10 (1.72)
45     14    399    550 ( 58.82)     0  0    0   0   0   0     0 (0.00)    0   10 (1.82)
44     19    418    536 ( 57.33)     0  0    0   0   0   0     0 (0.00)    0   10 (1.87)
43     40    458    517 ( 55.29)     0  0    0   0   0   0     0 (0.00)    0   10 (1.93)
42    107    565    477 ( 51.02)     0  0    0   0   0   0     0 (0.00)    0   10 (2.10)
41      5    570    370 ( 39.57)     0  0    0   0   0   0     0 (0.00)    0   10 (2.70)
40     82    652    365 ( 39.04)     0  0    0   0   0   0     0 (0.00)    0   10 (2.74)
39      9    661    283 ( 30.27)     0  0    0   0   0   0     0 (0.00)    0   10 (3.53)
38      3    664    274 ( 29.30)     0  0    0   0   0   0     0 (0.00)    0   10 (3.65)
37     55    719    271 ( 28.98)     0  0    0   0   0   0     0 (0.00)    0   10 (3.69)
36      1    720    216 ( 23.10)     0  0    0   0   0   0     0 (0.00)    0   10 (4.63)
35     53    773    215 ( 22.99)     0  0    0   0   0   0     0 (0.00)    0   10 (4.65)
34     14    787    162 ( 17.33)     0  0    0   0   0   0     0 (0.00)    0   10 (6.17)
33      9    796    148 ( 15.83)     0  0    0   0   0   0     0 (0.00)    0   10 (6.76)
32      8    804    139 ( 14.87)     0  0    0   0   0   0     0 (0.00)    0   10 (7.19)
31      7    811    131 ( 14.01)     0  0    0   0   0   0     0 (0.00)    0   10 (7.63)
30      4    815    124 ( 13.26)     0  0    0   0   0   0     0 (0.00)    0   10 (8.06)
29     24    839    120 ( 12.83)     0  0    0   0   0   0     0 (0.00)    0   10 (8.33)
28      3    842     96 ( 10.27)     0  0    0   0   0   0     0 (0.00)    0   10 (10.42)
27      8    850     93 (  9.95)     0  0    0   0   0   0     0 (0.00)    0   10 (10.75)
26      0    850     85 (  9.09)     0  0    0   0   0   0     0 (0.00)    0   10 (11.76)
25      6    856     85 (  9.09)     0  0    0   0   0   0     0 (0.00)    0   10 (11.76)
24      6    862     79 (  8.45)     0  0    0   0   0   0     0 (0.00)    0   10 (12.66)
23      6    868     73 (  7.81)     0  0    0   0   0   0     0 (0.00)    0   10 (13.70)
22      0    868     67 (  7.17)     0  0    0   0   0   0     0 (0.00)    0   10 (14.93)
21      7    875     67 (  7.17)     0  0    0   0   0   0     0 (0.00)    0   10 (14.93)
20      6    881     60 (  6.42)     0  0    0   0   0   0     0 (0.00)    0   10 (16.67)
19      4    885     54 (  5.78)     0  0    0   0   0   0     0 (0.00)    0   10 (18.52)
18      5    890     50 (  5.35)     0  0    0   0   0   0     0 (0.00)    0   10 (20.00)
17      0    890     45 (  4.81)     0  0    0   0   0   0     0 (0.00)    0   10 (22.22)
16      0    890     45 (  4.81)     0  0    0   0   0   0     0 (0.00)    0   10 (22.22)
15      2    892     45 (  4.81)     0  0    0   0   0   0     0 (0.00)    0   10 (22.22)
14      2    894     43 (  4.60)     0  0    0   0   0   0     0 (0.00)    0   10 (23.26)
13      1    895     41 (  4.39)     0  0    0   0   0   0     0 (0.00)    0   10 (24.39)
12      2    897     40 (  4.28)     0  0    0   0   0   0     0 (0.00)    0   10 (25.00)
11      6    903     38 (  4.06)     0  0    0   0   0   0     0 (0.00)    0   10 (26.32)
10      3    906     32 (  3.42)     0  0    0   1   0   0     1 (33.33)    1   10 (31.25)
 9      9    915     29 (  3.10)     1  0    0   1   0   0     1 (11.11)    2    9 (31.03)
 8     12    927     20 (  2.14)     1  0    0   7   0   0     7 (58.33)    9    8 (40.00)
 7      7    934      8 (  0.86)     2  0    0   0   1   0     1 (14.29)   10    1 (12.50)
 6      0    934      1 (  0.11)     2  0    0   0   0   0     0 (0.00)   10    0 (0.00)
 4      1    935      1 (  0.11)     0  0    0   0   0   0     0 (0.00)   10    0 (0.00)
-1      0    935      0 (  0.00)     0  0    0   0   0   0     0 (0.00)   10    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90    717    717    931 (100.00)     0  0    0   0   0   0     0 (0.00)    0    9 (0.97)
89     10    727    214 ( 22.99)     0  0    0   0   0   0     0 (0.00)    0    9 (4.21)
87     16    743    204 ( 21.91)     0  0    0   0   0   0     0 (0.00)    0    9 (4.41)
86     11    754    188 ( 20.19)     0  0    0   0   0   0     0 (0.00)    0    9 (4.79)
85     11    765    177 ( 19.01)     0  0    0   0   0   0     0 (0.00)    0    9 (5.08)
84     11    776    166 ( 17.83)     0  0    0   0   0   0     0 (0.00)    0    9 (5.42)
81     22    798    155 ( 16.65)     0  0    0   0   0   0     0 (0.00)    0    9 (5.81)
80      1    799    133 ( 14.29)     0  0    0   0   0   0     0 (0.00)    0    9 (6.77)
77      1    800    132 ( 14.18)     0  0    0   0   0   0     0 (0.00)    0    9 (6.82)
71      2    802    131 ( 14.07)     0  0    0   0   0   0     0 (0.00)    0    9 (6.87)
68      1    803    129 ( 13.86)     0  0    0   0   0   0     0 (0.00)    0    9 (6.98)
67      4    807    128 ( 13.75)     0  0    0   0   0   0     0 (0.00)    0    9 (7.03)
66     12    819    124 ( 13.32)     0  0    0   0   0   0     0 (0.00)    0    9 (7.26)
65      7    826    112 ( 12.03)     0  0    0   0   0   0     0 (0.00)    0    9 (8.04)
61      4    830    105 ( 11.28)     0  0    0   0   0   0     0 (0.00)    0    9 (8.57)
60     12    842    101 ( 10.85)     0  0    0   0   0   0     0 (0.00)    0    9 (8.91)
59      1    843     89 (  9.56)     0  0    0   0   0   0     0 (0.00)    0    9 (10.11)
58      1    844     88 (  9.45)     0  0    0   0   0   0     0 (0.00)    0    9 (10.23)
57      3    847     87 (  9.34)     0  0    0   0   0   0     0 (0.00)    0    9 (10.34)
56      3    850     84 (  9.02)     0  0    0   0   0   0     0 (0.00)    0    9 (10.71)
55      3    853     81 (  8.70)     0  0    0   0   0   0     0 (0.00)    0    9 (11.11)
54      7    860     78 (  8.38)     0  0    0   0   0   0     0 (0.00)    0    9 (11.54)
53      4    864     71 (  7.63)     0  0    0   0   0   0     0 (0.00)    0    9 (12.68)
52      2    866     67 (  7.20)     0  0    0   0   0   0     0 (0.00)    0    9 (13.43)
50      2    868     65 (  6.98)     0  0    0   0   0   0     0 (0.00)    0    9 (13.85)
49      1    869     63 (  6.77)     0  0    0   0   0   0     0 (0.00)    0    9 (14.29)
48      3    872     62 (  6.66)     0  0    0   0   0   0     0 (0.00)    0    9 (14.52)
46      1    873     59 (  6.34)     0  0    0   0   0   0     0 (0.00)    0    9 (15.25)
45      6    879     58 (  6.23)     0  0    0   0   0   0     0 (0.00)    0    9 (15.52)
44      5    884     52 (  5.59)     0  0    0   0   0   0     0 (0.00)    0    9 (17.31)
43      2    886     47 (  5.05)     0  0    0   0   0   0     0 (0.00)    0    9 (19.15)
40      8    894     45 (  4.83)     0  0    0   0   0   0     0 (0.00)    0    9 (20.00)
29      1    895     37 (  3.97)     0  0    0   0   0   0     0 (0.00)    0    9 (24.32)
24      1    896     36 (  3.87)     0  0    0   0   0   0     0 (0.00)    0    9 (25.00)
23      1    897     35 (  3.76)     0  0    0   0   0   0     0 (0.00)    0    9 (25.71)
21      1    898     34 (  3.65)     0  0    0   0   0   0     0 (0.00)    0    9 (26.47)
20      1    899     33 (  3.54)     0  0    0   0   0   0     0 (0.00)    0    9 (27.27)
19      1    900     32 (  3.44)     0  0    0   0   0   0     0 (0.00)    0    9 (28.12)
15     14    914     31 (  3.33)     0  0    0   6   0   0     6 (42.86)    6    9 (29.03)
13      1    915     17 (  1.83)     0  0    0   0   0   0     0 (0.00)    6    3 (17.65)
11      3    918     16 (  1.72)     0  0    0   0   0   0     0 (0.00)    6    3 (18.75)
10      3    921     13 (  1.40)     0  0    0   1   0   0     1 (33.33)    7    3 (23.08)
 9      2    923     10 (  1.07)     0  0    0   1   0   0     1 (50.00)    8    2 (20.00)
 8      3    926      8 (  0.86)     0  0    0   0   0   0     0 (0.00)    8    1 (12.50)
 7      5    931      5 (  0.54)     0  0    0   0   1   0     1 (20.00)    9    1 (20.00)
-1      4    935      0 (  0.00)     6  0    0   1   0   0     1 (25.00)   10    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
 43       1        1        1
 44       1        2        1
 46       1        3        2
 55       2        5        2
 56       2        7        3
 60       5       12        4
 61       2       14        3
 66       5       19        3
 67       2       21        4
 81      11       32        4
 84       3       35        6
 85       3       38        7
 86       3       41        6
 87       4       45        7
 89       3       48        9
 90     187      235        1

SS region: 3 (1.28%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
  235     -4.0  [-4.0,  0.0]  (0, 1)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 14.  86 reads; 8324 bp (untrimmed), 7807 (trimmed).
      1   991 ee060109r1    892 (  0)  0.41 1.04 0.00    0 (203)   25 ( 57) 
    180  1195 af110109f1    811 (  0)  0.45 1.02 0.00   24 ( 24)  112 (112) 
    303  1316 be100109r1    866 (  0)  1.47 0.42 0.11   48 ( 48)   14 ( 91) 
    466  1449 ee040109r1    872 (  0)  0.96 0.53 0.00   47 ( 47)    1 ( 52) 
    592  1658 aa070109r1    757 (  0)  0.46 2.20 0.12   49 ( 49)  154 (239) 
    793  1760 ea080109r1    828 (  0)  1.31 0.76 0.00   45 ( 45)    4 ( 54) 
    848  1907 dh040109f1    812 (  0)  1.10 0.99 0.00   51 ( 51)  100 (133) 
    919  1980 ce050109r1    796 (  0)  1.55 0.88 0.00   47 ( 47)  111 (161) 
    932  1965 db100109r1    796 (  0)  0.68 1.13 0.00   50 ( 50)   98 ( 95) 
C  1044  2119 de050109r1    758 (  0)  0.61 0.37 0.00  209 (201)   49 ( 49) 
   1065  2066 cd120109f1    815 (  0)  2.28 0.62 0.31   37 ( 37)    2 ( 38) 
   1154  2179 bc020109r1    784 (  0)  1.55 0.99 0.00   47 ( 47)   74 (103) 
   1204  2288 de050109f1    750 (  0)  0.73 0.24 0.12   49 ( 42)  218 (218) 
   1251  2176 eh120109r1    812 (  0)  1.02 0.23 0.00   45 ( 45)    0 ( 32) 
   1321  2348 dh120109r1    751 (  0)  1.51 0.93 0.00   60 ( 60)  107 (107) 
   1322  2312 cf010109r1    802 (  0)  1.81 1.28 0.00   44 ( 44)   10 (107) 
   1335  2376 bc060109r1    865 (  0)  1.14 0.41 0.31   47 ( 47)   30 ( 54) 
   1337  2345 bh090109f1    753 (  0)  0.94 0.94 0.12   35 ( 35)  119 (135) 
C  1447  2433 ee060109f1    901 (  0)  0.31 0.31 0.00   10 ( 10)   19 ( 19) 
C  1521  2530 af110109r1    824 (  0)  1.37 1.58 0.00   14 ( 53)   45 ( 45) 
   1512  2518 ec040109f1    876 (  0)  1.83 0.20 0.41   23 ( 23)    0 ( 47) 
C  1527  2543 cd120109r1    774 (  0)  1.84 0.69 0.00   97 (122)   50 ( 50) 
   1536  2562 be080109f1    854 (  0)  0.86 0.75 0.00   33 ( 44)   62 ( 93) 
   1696  2693 ce120109r1    855 (  0)  1.17 0.74 0.21   48 ( 48)   10 ( 44) 
   1903  2878 ag120109r1    762 (  0)  4.46 0.54 0.00   47 ( 47)   10 (110) 
   1951  2969 ch060109f1    909 (  0)  1.21 0.40 0.40   26 ( 26)    3 ( 26) 
   1960  2952 db110109f1    875 (  0)  1.16 0.53 0.21   29 ( 29)   16 ( 16) 
C  1999  2994 be100109f1    900 (  0)  0.72 0.93 0.10    4 ( 15)   21 ( 20) 
C  1999  3020 db100109f1    855 (  0)  2.53 0.91 0.20    4 ( 88)   31 ( 31) 
C  2007  3001 ce120109f1    895 (  0)  1.34 0.72 0.00    1 ( 34)   23 ( 23) 
   2034  3038 ch110109f1    892 (  0)  1.34 0.62 0.10   30 ( 30)    8 ( 51) 
   2093  3073 bg120109f1    839 (  0)  1.41 0.98 0.00   29 ( 29)   33 ( 54) 
   2173  3196 ce100109r1    883 (  0)  1.77 0.42 0.10   51 ( 51)   14 ( 62) 
C  2306  3340 dh040109r1    789 (  0)  1.70 1.14 0.00  107 (137)   47 ( 47) 
   2480  3441 ed010109f1    908 (  0)  0.11 0.43 0.00   23 ( 23)    1 (  1) 
C  2496  3531 bc020109f1    673 (  0)  3.17 1.34 0.12  197 (309)   20 ( 20) 
C  2495  3569 ce050109f1    871 (  0)  1.74 0.92 0.10   46 ( 54)   53 ( 53) 
   2490  3562 dc030109r1    825 (  0)  1.10 1.10 0.00   49 ( 49)  117 (117) 
C  2550  3484 eh120109f1    852 (  0)  0.77 0.33 0.22    4 (  4)   25 ( 25) 
   2596  3642 cc030109f1    886 (  0)  1.50 1.40 0.00   23 ( 21)   21 ( 94) 
C  2674  3743 dc030109f1    859 (  0)  1.35 1.04 0.21   71 (145)   35 ( 35) 
C  2809  3784 ea080109f1    888 (  0)  0.53 0.74 0.00    0 (  0)   32 ( 52) 
C  2829  3834 cf010109f1    816 (  0)  1.52 1.30 0.00   56 (169)   27 ( 27) 
C  3083  4094 bh090109r1    797 (  0)  2.43 1.16 0.00    7 ( 64)   57 ( 57) 
C  3132  4301 aa070109f1    784 (  0)  0.66 1.65 0.00  122 (163)  139 (139) 
C  3191  4179 ee040109f1    881 (  0)  0.42 0.62 0.00    1 ( 32)   26 ( 26) 
C  3391  4413 bc060109f1    862 (  0)  1.42 0.81 0.00    6 ( 35)   29 ( 28) 
C  3409  4517 dh120109f1    776 (  0)  1.68 2.10 0.00   22 ( 92)  133 (132) 
C  3469  4470 ch110109r1    802 (  0)  0.67 0.56 0.22   57 ( 17)   47 ( 47) 
C  3551  4532 db110109r1    774 (  0)  1.93 1.18 0.11    5 ( 51)   46 ( 46) 
C  3581  4588 ec040109r1    819 (  0)  0.63 1.78 0.00    6 ( 70)   47 ( 47) 
C  3574  4548 ag120109f1    794 (  0)  2.13 0.75 0.00   10 ( 63)   28 ( 28) 
C  3575  4591 ch060109r1    822 (  0)  1.47 0.73 0.10   18 ( 52)   46 ( 46) 
   3677  4721 bg030109r1    756 (  0)  0.34 1.59 0.00   45 ( 45)  120 (161) 
C  3765  4724 eh110109f1    720 (  0)  0.25 0.12 0.12  132 (132)   27 ( 14) 
C  3823  4841 ce100109f1    851 (  0)  0.62 0.62 0.00   22 ( 22)   32 ( 32) 
   3848  4787 eh110109r1    718 (  0)  0.75 0.00 0.00   48 ( 48)   90 ( 77) 
C  3922  4911 bg120109r1    731 (  0)  1.97 1.42 0.22   27 ( 53)   49 ( 83) 
   3966  4954 ba100109f1    782 (  0)  1.79 1.26 0.11   30 ( 42)    9 (  9) 
   4262  5418 da060109f1    696 (  0)  2.09 1.63 0.12  116 (116)  180 (235) 
C  4363  5428 be080109r1    794 (  0)  0.22 1.12 0.00  127 (101)   49 ( 49) 
   4381  5408 cb090109f1    822 (  0)  2.23 1.01 0.20   34 ( 34)    7 ( 12) 
C  4434  5481 cc030109r1    832 (  0)  1.62 1.21 0.10    4 ( 38)   56 ( 56) 
   4476  5533 dg060109f1    774 (  0)  1.56 2.28 0.10   50 ( 50)   45 (147) 
   4496  5513 ae010109r1    752 (  0)  1.74 1.63 0.11   48 ( 48)   52 ( 88) 
   4523  5571 ae020109r1    782 (  0)  1.10 1.21 0.11   49 ( 49)   92 (157) 
   4543  5565 df090109f1    836 ( 33)  2.12 1.01 0.10   29 ( 29)    3 ( 90) 
C  4567  5615 ag040109f1    132 (136)  0.69 0.00 0.69  874 (874)   30 ( 30) 
   4598  5626 bb060109r1    851 ( 73)  2.14 0.51 0.20   47 ( 47)    0 ( 89) 
C  5116  6129 bg030109f1    780 (  0)  0.98 1.85 0.00   73 (121)   24 ( 24) 
C  5133  6089 ed010109r1    837 (  0)  0.55 0.33 0.11    0 (  0)   47 ( 47) 
C  5509  6508 ba100109r1    771 (  0)  2.34 0.96 0.00   16 ( 44)   43 ( 43) 
C  5755  6873 da060109r1    718 (  0)  2.06 1.03 0.00  128 (191)  118 (118) 
C  5832  6857 bb060109f1    788 (  0)  0.87 0.87 0.11   87 ( 87)   23 ( 23) 
C  5876  6898 cb090109r1    804 ( 33)  1.45 1.24 0.00    7 (112)   48 ( 48) 
C  5915  6938 ae020109f1    811 ( 36)  2.42 0.61 0.10    3 ( 28)   30 ( 30) 
   5963  6960 de110109f1    836 ( 33)  1.15 0.21 0.10   29 ( 29)   10 (  4) 
   5988  6954 ec020109r1    823 ( 37)  0.44 0.00 0.00   45 ( 45)    7 (  0) 
   6007  6962 eg100109r1    796 ( 33)  0.77 0.00 0.33   47 ( 47)    4 (  6) 
C  6146  7143 ae010109f1    788 ( 36)  2.00 0.63 0.32   22 ( 93)   25 ( 25) 
   6432  7520 dd070109f1    749 ( 36)  0.99 1.43 0.00   26 ( 26)  157 (157) 
C  6469  7491 df090109r1    784 ( 36)  1.36 0.94 0.10   19 ( 68)   49 ( 49) 
C  6561  7641 dg060109r1    660 (  0)  0.59 2.37 0.12  189 (231)   49 ( 49) 
   6771  7724 ee110109f1    789 (  0)  0.86 0.65 0.00   26 ( 31)    0 (  0) 
   7014  8090 ab040109f1    690 (  0)  4.63 0.77 0.48   40 ( 40)    1 (206) 
   7253  8324 be040109r1    816 (  0)  0.29 0.00 0.00   43 ( 43)    0 (438) 

Overall discrep rates (%):             1.36 0.90 0.09

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90    5006  60.1    5006  60.1    0.00
 89      27   0.3    5033  60.5    0.00
 88      17   0.2    5050  60.7    0.00
 87      17   0.2    5067  60.9    0.00
 86      14   0.2    5081  61.0    0.00
 85      20   0.2    5101  61.3    0.00
 84      25   0.3    5126  61.6    0.00
 83      19   0.2    5145  61.8    0.00
 82      16   0.2    5161  62.0    0.00
 81      98   1.2    5259  63.2    0.00
 80      10   0.1    5269  63.3    0.00
 79      23   0.3    5292  63.6    0.00
 78      11   0.1    5303  63.7    0.00
 77      20   0.2    5323  63.9    0.00
 76      31   0.4    5354  64.3    0.00
 75      36   0.4    5390  64.8    0.00
 74       9   0.1    5399  64.9    0.00
 73      16   0.2    5415  65.1    0.00
 72      13   0.2    5428  65.2    0.00
 71       7   0.1    5435  65.3    0.00
 70       4   0.0    5439  65.3    0.00
 69      11   0.1    5450  65.5    0.00
 68      10   0.1    5460  65.6    0.00
 67      12   0.1    5472  65.7    0.00
 66    1535  18.4    7007  84.2    0.00
 65       4   0.0    7011  84.2    0.00
 64       1   0.0    7012  84.2    0.00
 63       5   0.1    7017  84.3    0.00
 62       3   0.0    7020  84.3    0.00
 61     293   3.5    7313  87.9    0.00
 60      54   0.6    7367  88.5    0.00
 59       1   0.0    7368  88.5    0.00
 58       4   0.0    7372  88.6    0.00
 57       5   0.1    7377  88.6    0.00
 56      68   0.8    7445  89.4    0.00
 55      23   0.3    7468  89.7    0.00
 54      39   0.5    7507  90.2    0.00
 53      27   0.3    7534  90.5    0.00
 52      43   0.5    7577  91.0    0.00
 51      39   0.5    7616  91.5    0.00
 50      18   0.2    7634  91.7    0.00
 48      12   0.1    7646  91.9    0.00
 47      16   0.2    7662  92.0    0.00
 46       2   0.0    7664  92.1    0.00
 45      32   0.4    7696  92.5    0.00
 44      11   0.1    7707  92.6    0.00
 43      12   0.1    7719  92.7    0.00
 42      21   0.3    7740  93.0    0.01
 40      15   0.2    7755  93.2    0.01
 39       3   0.0    7758  93.2    0.01
 38       1   0.0    7759  93.2    0.01
 37      16   0.2    7775  93.4    0.01
 36       1   0.0    7776  93.4    0.01
 35      12   0.1    7788  93.6    0.02
 33       6   0.1    7794  93.6    0.02
 32       5   0.1    7799  93.7    0.02
 31       1   0.0    7800  93.7    0.02
 29       2   0.0    7802  93.7    0.02
 28       2   0.0    7804  93.8    0.03
 26       1   0.0    7805  93.8    0.03
 24       1   0.0    7806  93.8    0.03
 19       1   0.0    7807  93.8    0.05
 -1     517   6.2    8324 100.0  517.05   (quality -1 = terminal quality 0)

Avg. full length: 8324.0, trimmed (qual > -1): 7807.0
Avg. quality: 76.0 per base

Initial, terminal qual 0 segments:  1-80, 7888-8324

Regions of LLR- adjusted quality < 2.0:
1-80, 7887-8324, 

2 regions, avg size 259.0, avg spacing 4162.0

First_start: 204, last_end: 7886

Slack, # used pairs (max_score), unused
 0   192  (20.6)     0 ( 0.0)      778
 1   280  (20.8)     0 ( 0.0)       78
 2   139  (20.7)     0 ( 0.0)        1
 3    88  (20.2)     0 ( 0.0)        0
 4    60  (20.1)     0 ( 0.0)        0
 5    29  (19.7)     0 ( 0.0)        0
 6    21  (18.1)     0 ( 0.0)        0
 7    10  (17.9)     0 ( 0.0)        0
 8    11  (18.5)     0 ( 0.0)        0
 9    11  (18.4)     0 ( 0.0)        0
10     8  (18.4)     0 ( 0.0)        0
11     5  (18.1)     0 ( 0.0)        0
12     3  (14.3)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 3622 -  3721      100       cc030109f1   (2596)    No           1126
 5627 -  5991      365       bb060109r1   (4598)    No           1394
 8325 - right        0+      be040109r1   (7253)    No           1071+

Bottom strand: 
 left -  1252     1252+      de050109r1   (2119)    No           2119+
 7593 - right      732+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56  20514  20514  79423 (100.00)     8  0    0   0   0   0     0 (0.00)    0  1828 (2.30)
51   4688  25202  58909 ( 74.17)     1  0    0   0   0   0     0 (0.00)    0  1828 (3.10)
50   3933  29135  54221 ( 68.27)     0  0    0   0   0   0     0 (0.00)    0  1828 (3.37)
48    337  29472  50288 ( 63.32)     2  0    0   0   0   0     0 (0.00)    0  1828 (3.64)
47    619  30091  49951 ( 62.89)     1  0    0   0   0   0     0 (0.00)    0  1828 (3.66)
46   1017  31108  49332 ( 62.11)     5  0    0   0   0   0     0 (0.00)    0  1828 (3.71)
45    926  32034  48315 ( 60.83)     0  0    0   0   0   0     0 (0.00)    0  1828 (3.78)
44   2765  34799  47389 ( 59.67)     2  0    0   0   0   0     0 (0.00)    0  1828 (3.86)
43   1993  36792  44624 ( 56.19)     4  0    0   0   0   0     0 (0.00)    0  1828 (4.10)
42   5677  42469  42631 ( 53.68)    10  0    0   0   0   0     0 (0.00)    0  1828 (4.29)
41    566  43035  36954 ( 46.53)     0  0    0   0   0   0     0 (0.00)    0  1828 (4.95)
40   3684  46719  36388 ( 45.82)    34  0    0   0   0   0     0 (0.00)    0  1828 (5.02)
39    172  46891  32704 ( 41.18)     2  0    0   0   0   0     0 (0.00)    0  1828 (5.59)
38    315  47206  32532 ( 40.96)     1  0    0   0   0   0     0 (0.00)    0  1828 (5.62)
37   1624  48830  32217 ( 40.56)     8  0    0   0   0   0     0 (0.00)    0  1828 (5.67)
36    153  48983  30593 ( 38.52)     3  0    0   0   0   0     0 (0.00)    0  1828 (5.98)
35   1274  50257  30440 ( 38.33)     4  0    0   0   0   0     0 (0.00)    0  1828 (6.01)
34    666  50923  29166 ( 36.72)     4  0    0   0   0   0     0 (0.00)    0  1828 (6.27)
33    698  51621  28500 ( 35.88)    10  0    0   0   0   0     0 (0.00)    0  1828 (6.41)
32    775  52396  27802 ( 35.00)    22  0    0   0   0   1     1 (0.13)    1  1828 (6.58)
31    273  52669  27027 ( 34.03)     4  0    0   0   0   0     0 (0.00)    1  1827 (6.76)
30    367  53036  26754 ( 33.69)     4  0    0   0   0   0     0 (0.00)    1  1827 (6.83)
29   1524  54560  26387 ( 33.22)    29  0    0   0   1   2     3 (0.20)    4  1827 (6.92)
28    387  54947  24863 ( 31.30)     3  0    0   0   0   0     0 (0.00)    4  1824 (7.34)
27    615  55562  24476 ( 30.82)    20  0    0   1   1   1     3 (0.49)    7  1824 (7.45)
26    228  55790  23861 ( 30.04)    20  0    0   0   1   0     1 (0.44)    8  1821 (7.63)
25    856  56646  23633 ( 29.76)    31  0    0   0   0   0     0 (0.00)    8  1820 (7.70)
24    612  57258  22777 ( 28.68)    27  0    0   0   0   0     0 (0.00)    8  1820 (7.99)
23    540  57798  22165 ( 27.91)    15  0    0   0   2   0     2 (0.37)   10  1820 (8.21)
22    417  58215  21625 ( 27.23)    24  0    0   0   4   0     4 (0.96)   14  1818 (8.41)
21    630  58845  21208 ( 26.70)    29  0    0   1   1   0     2 (0.32)   16  1814 (8.55)
20    600  59445  20578 ( 25.91)    35  0    0   0   2   0     2 (0.33)   18  1812 (8.81)
19    840  60285  19978 ( 25.15)    68  0    0   1   2   0     3 (0.36)   21  1810 (9.06)
18    682  60967  19138 ( 24.10)    47  0    0   0   7   1     8 (1.17)   29  1807 (9.44)
17    653  61620  18456 ( 23.24)    29  0    0   5   4   2    11 (1.68)   40  1799 (9.75)
16    684  62304  17803 ( 22.42)    65  0    0   4   3   0     7 (1.02)   47  1788 (10.04)
15   1020  63324  17119 ( 21.55)    58  0    0   8   5   1    14 (1.37)   61  1781 (10.40)
14    726  64050  16099 ( 20.27)    56  0    0  10   5   0    15 (2.07)   76  1767 (10.98)
13   1089  65139  15373 ( 19.36)    76  0    0  14  14   4    32 (2.94)  108  1752 (11.40)
12   1164  66303  14284 ( 17.98)    89  0    0  27  21   6    54 (4.64)  162  1720 (12.04)
11   1554  67857  13120 ( 16.52)   114  0    0  54  30   6    90 (5.79)  252  1666 (12.70)
10   2101  69958  11566 ( 14.56)   173  0    0  90  54   6   150 (7.14)  402  1576 (13.63)
 9   3528  73486   9465 ( 11.92)   290  0    0 215 104  19   338 (9.58)  740  1426 (15.07)
 8   2529  76015   5937 (  7.48)   214  0    0 231 149  10   390 (15.42)  1130  1088 (18.33)
 7   2186  78201   3408 (  4.29)   193  0    0 250 150   4   404 (18.48)  1534  698 (20.48)
 6   1151  79352   1222 (  1.54)   111  0    0 156 111   6   273 (23.72)  1807  294 (24.06)
 4     59  79411     71 (  0.09)     2  0    0   4   8   0    12 (20.34)  1819   21 (29.58)
 0     12  79423     12 (  0.02)   670  0    3   0   6   0     9 (75.00)  1828    9 (75.00)
-1    290  79713      0 (  0.00)  6100  0    0   0   6   0     6 (2.07)  1834    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90  52016  52016  75984 (100.00)     0  0    0   0   0   0     0 (0.00)    0  1175 (1.55)
89    241  52257  23968 ( 31.54)     0  0    0   0   0   0     0 (0.00)    0  1175 (4.90)
88    160  52417  23727 ( 31.23)     0  0    0   0   0   0     0 (0.00)    0  1175 (4.95)
87    128  52545  23567 ( 31.02)     0  0    0   0   0   0     0 (0.00)    0  1175 (4.99)
86    128  52673  23439 ( 30.85)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.01)
85    187  52860  23311 ( 30.68)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.04)
84    189  53049  23124 ( 30.43)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.08)
83    123  53172  22935 ( 30.18)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.12)
82     86  53258  22812 ( 30.02)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.15)
81    990  54248  22726 ( 29.91)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.17)
80     47  54295  21736 ( 28.61)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.41)
79     94  54389  21689 ( 28.54)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.42)
78     58  54447  21595 ( 28.42)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.44)
77     51  54498  21537 ( 28.34)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.46)
76    217  54715  21486 ( 28.28)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.47)
75     76  54791  21269 ( 27.99)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.52)
74     26  54817  21193 ( 27.89)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.54)
73     59  54876  21167 ( 27.86)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.55)
72     46  54922  21108 ( 27.78)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.57)
71     29  54951  21062 ( 27.72)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.58)
70     17  54968  21033 ( 27.68)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.59)
69     36  55004  21016 ( 27.66)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.59)
68     34  55038  20980 ( 27.61)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.60)
67     55  55093  20946 ( 27.57)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.61)
66   8206  63299  20891 ( 27.49)     0  0    0   0   0   0     0 (0.00)    0  1175 (5.62)
65    179  63478  12685 ( 16.69)     0  0    0   0   0   0     0 (0.00)    0  1175 (9.26)
64     13  63491  12506 ( 16.46)     0  0    0   0   0   0     0 (0.00)    0  1175 (9.40)
63     10  63501  12493 ( 16.44)     0  0    0   0   0   0     0 (0.00)    0  1175 (9.41)
62     46  63547  12483 ( 16.43)     0  0    0   0   0   0     0 (0.00)    0  1175 (9.41)
61   1264  64811  12437 ( 16.37)     0  0    0   0   0   0     0 (0.00)    0  1175 (9.45)
60    149  64960  11173 ( 14.70)     0  0    0   0   0   0     0 (0.00)    0  1175 (10.52)
59     40  65000  11024 ( 14.51)     0  0    0   0   0   0     0 (0.00)    0  1175 (10.66)
58     71  65071  10984 ( 14.46)     0  0    0   0   0   0     0 (0.00)    0  1175 (10.70)
57     81  65152  10913 ( 14.36)     0  0    0   0   0   0     0 (0.00)    0  1175 (10.77)
56    161  65313  10832 ( 14.26)     0  0    0   0   0   0     0 (0.00)    0  1175 (10.85)
55    106  65419  10671 ( 14.04)     0  0    0   0   0   0     0 (0.00)    0  1175 (11.01)
54    180  65599  10565 ( 13.90)     0  0    0   0   0   0     0 (0.00)    0  1175 (11.12)
53    109  65708  10385 ( 13.67)     0  0    0   0   0   0     0 (0.00)    0  1175 (11.31)
52    195  65903  10276 ( 13.52)     0  0    0   0   0   0     0 (0.00)    0  1175 (11.43)
51     70  65973  10081 ( 13.27)     0  0    0   0   0   0     0 (0.00)    0  1175 (11.66)
50    173  66146  10011 ( 13.18)     0  0    0   0   0   0     0 (0.00)    0  1175 (11.74)
49     78  66224   9838 ( 12.95)     0  0    0   0   0   0     0 (0.00)    0  1175 (11.94)
48     77  66301   9760 ( 12.84)     0  0    0   0   0   0     0 (0.00)    0  1175 (12.04)
47     68  66369   9683 ( 12.74)     0  0    0   0   0   0     0 (0.00)    0  1175 (12.13)
46     71  66440   9615 ( 12.65)     0  0    0   0   0   0     0 (0.00)    0  1175 (12.22)
45    120  66560   9544 ( 12.56)     0  0    0   0   0   0     0 (0.00)    0  1175 (12.31)
44    120  66680   9424 ( 12.40)     0  0    0   0   0   0     0 (0.00)    0  1175 (12.47)
43     84  66764   9304 ( 12.24)     0  0    0   0   0   0     0 (0.00)    0  1175 (12.63)
42    136  66900   9220 ( 12.13)     0  0    0   0   0   0     0 (0.00)    0  1175 (12.74)
41     82  66982   9084 ( 11.96)     0  0    0   0   0   0     0 (0.00)    0  1175 (12.93)
40   1856  68838   9002 ( 11.85)     0  0    0   0   0   0     0 (0.00)    0  1175 (13.05)
39     53  68891   7146 (  9.40)     0  0    0   0   0   0     0 (0.00)    0  1175 (16.44)
38     30  68921   7093 (  9.33)     0  0    0   0   0   0     0 (0.00)    0  1175 (16.57)
37     63  68984   7063 (  9.30)     0  0    0   0   0   0     0 (0.00)    0  1175 (16.64)
36     33  69017   7000 (  9.21)     0  0    0   0   0   0     0 (0.00)    0  1175 (16.79)
35     84  69101   6967 (  9.17)     0  0    0   0   0   0     0 (0.00)    0  1175 (16.87)
34     88  69189   6883 (  9.06)     1  0    0   0   0   0     0 (0.00)    0  1175 (17.07)
33     73  69262   6795 (  8.94)     0  0    0   0   0   0     0 (0.00)    0  1175 (17.29)
32     81  69343   6722 (  8.85)     0  0    0   0   0   1     1 (1.23)    1  1175 (17.48)
31     42  69385   6641 (  8.74)     0  0    0   0   0   0     0 (0.00)    1  1174 (17.68)
30     23  69408   6599 (  8.68)     0  0    0   0   0   0     0 (0.00)    1  1174 (17.79)
29     75  69483   6576 (  8.65)     0  0    0   0   1   1     2 (2.67)    3  1174 (17.85)
28     20  69503   6501 (  8.56)     1  0    0   0   0   0     0 (0.00)    3  1172 (18.03)
27     61  69564   6481 (  8.53)     1  0    0   0   1   1     2 (3.28)    5  1172 (18.08)
26     42  69606   6420 (  8.45)     0  0    0   0   1   0     1 (2.38)    6  1170 (18.22)
25    596  70202   6378 (  8.39)     0  0    0   0   0   0     0 (0.00)    6  1169 (18.33)
24     80  70282   5782 (  7.61)     2  0    0   0   1   0     1 (1.25)    7  1169 (20.22)
23     77  70359   5702 (  7.50)     1  0    0   0   4   0     4 (5.19)   11  1168 (20.48)
22     37  70396   5625 (  7.40)     0  0    0   0   4   0     4 (10.81)   15  1164 (20.69)
21     75  70471   5588 (  7.35)     4  0    0   1   2   0     3 (4.00)   18  1160 (20.76)
20     61  70532   5513 (  7.26)     0  0    0   0   2   0     2 (3.28)   20  1157 (20.99)
19    112  70644   5452 (  7.18)     1  0    0   2   2   0     4 (3.57)   24  1155 (21.18)
18     55  70699   5340 (  7.03)     6  0    0   0   7   1     8 (14.55)   32  1151 (21.55)
17     83  70782   5285 (  6.96)     0  0    0   2   3   2     7 (8.43)   39  1143 (21.63)
16    110  70892   5202 (  6.85)     6  0    0   1   2   0     3 (2.73)   42  1136 (21.84)
15    152  71044   5092 (  6.70)     6  0    0   4   7   1    12 (7.89)   54  1133 (22.25)
14    127  71171   4940 (  6.50)     9  0    0   3   3   0     6 (4.72)   60  1121 (22.69)
13    256  71427   4813 (  6.33)     8  0    0  11  11   4    26 (10.16)   86  1115 (23.17)
12    245  71672   4557 (  6.00)    12  0    0  12  19   5    36 (14.69)  122  1089 (23.90)
11    392  72064   4312 (  5.67)     9  0    0  28  21   5    54 (13.78)  176  1053 (24.42)
10    604  72668   3920 (  5.16)     9  0    0  48  33   5    86 (14.24)  262  999 (25.48)
 9   1120  73788   3316 (  4.36)    15  0    0 142  59  16   217 (19.38)  479  913 (27.53)
 8    838  74626   2196 (  2.89)    12  0    0 156  95   6   257 (30.67)  736  696 (31.69)
 7    874  75500   1358 (  1.79)    24  0    0 167 101   4   272 (31.12)  1008  439 (32.33)
 6    439  75939    484 (  0.64)     2  0    0  93  57   4   154 (35.08)  1162  167 (34.50)
 4     40  75979     45 (  0.06)     1  0    0   0   8   0     8 (20.00)  1170   13 (28.89)
 0      5  75984      5 (  0.01)     0  0    3   0   2   0     5 (100.00)  1175    5 (100.00)
-1   3729  79713      0 (  0.00)  8587  0    0 401 245  13   659 (17.67)  1834    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     517      517        2
 19       1      518        2
 24       1      519        2
 26       1      520        2
 28       2      522        4
 29       2      524        5
 31       1      525        6
 32       5      530        7
 33       6      536        6
 35      12      548        8
 36       1      549        7
 37      16      565        8
 38       1      566        8
 39       3      569        9
 40      15      584       11
 42      21      605       13
 43      12      617       15
 44      11      628       19
 45      32      660       23
 46       2      662       23
 47      16      678       24
 48      12      690       26
 50      18      708       23
 51      39      747       26
 52      43      790       42
 53      27      817       46
 54      39      856       50
 55      23      879       60
 56      68      947       52
 57       5      952       50
 58       4      956       51
 59       1      957       51
 60      54     1011       52
 61     293     1304       95
 62       3     1307       96
 63       5     1312       97
 64       1     1313       98
 65       4     1317       98
 66    1535     2852       24
 67      12     2864       25
 68      10     2874       26
 69      11     2885       26
 70       4     2889       25
 71       7     2896       27
 72      13     2909       30
 73      16     2925       38
 74       9     2934       39
 75      36     2970       40
 76      31     3001       40
 77      20     3021       42
 78      11     3032       41
 79      23     3055       32
 80      10     3065       32
 81      98     3163       48
 82      16     3179       47
 83      19     3198       49
 84      25     3223       51
 85      20     3243       48
 86      14     3257       48
 87      17     3274       48
 88      17     3291       51
 89      27     3318       53
 90    5006     8324        1

SS region: 2449 (29.42%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
 2494     -3.3  [-3.3,  0.0]  (0, 1)
 3294     -4.0  [-4.0,  0.0]  (0, 1)
 3699     -3.2  [-3.2,  0.0]  (0, 1)
 4038     -3.5  [-3.5,  0.0]  (0, 1)
 4487     -3.0  [-3.0,  0.0]  (0, 1)
 4863     -3.1  [-3.1,  0.0]  (0, 1)
 5380     -4.2  [-4.2,  0.0]  (0, 1)
 6466     -3.2  [-3.2,  0.0]  (0, 1)
 7593     -5.6  [-5.6,  0.0]  (0, 1)

Read/contig discrepancies (* = higher-quality):
  7901  S     ab040109f1      (0)/(0)  7900 CCT / CTT
  7910  S     ab040109f1      (0)/(0)  7904 TCCGTCAA / TTGCTTTTTA
  7916  D     ab040109f1      (0)/(0)  7914 TTAT / TTT
  7922  D     ab040109f1      (0)/(0)  7920 TTGT / TTT
  7928  I     ab040109f1      (0)/(0)  7928 AT / AAT
  7932  S     ab040109f1      (0)/(0)  7931 TCT / TTT
  7938  S     ab040109f1      (0)/(0)  7936 TTTT / TCCT
  7948  S     ab040109f1      (0)/(0)  7944 TACTGA / TTTTTA
  7954  D     ab040109f1      (0)/(0)  7952 TGGT / TGT
  7964  D     ab040109f1      (0)/(0)  7958 TTTATTAT / TTATTT
  7968  S     ab040109f1      (0)/(0)  7967 TCT / TAT
  7976  I     ab040109f1      (0)/(0)  7974 ACTC / ATTTC
  7994  S     ab040109f1      (0)/(0)  7988 TTCTATAT / TATTTTTT
  8001  I     ab040109f1      (0)/(0)  8001 TC / TAC
  8014  S     ab040109f1      (0)/(0)  8004 TCTTCTTTTTTT / TTTTTTTATTCT
  8023  S     ab040109f1      (0)/(0)  8020 TATAT / TTTTT
  8029  S     ab040109f1      (0)/(0)  8028 TTT / TCT
  8033  S     ab040109f1      (0)/(0)  8032 TCT / TTT
  8049  S     ab040109f1      (0)/(0)  8043 TATATTAT / TTTTCTTT
  8058  S     ab040109f1      (0)/(0)  8055 ACTCT / ATTTT
  8065  S     ab040109f1      (0)/(0)  8064 TTT / TCT
  8072  S     ab040109f1      (0)/(0)  8069 TCTAT / TTTTT

0 HQ discrepancies in 0 reads.
22 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)  5441- 5585 [ 2.8] (0,0)   C ag040109f1         174-31 | 16 174  (881 936) | DU:(881 936) [881 936  with   dd100109f1  990 1044]  || local(+/-) (3.0,0.0), distant (2.9,1.1)

Gaps in unique-read coverage:  None.

Contig 15.  100 reads; 9407 bp (untrimmed), 9266 (trimmed).
C   -56   966 ec020109f1    582 ( 37)  2.12 0.00 0.15  339 (395)   25 ( 25) 
      1  1138 da090109r1    911 (  0)  0.85 1.23 0.09    0 (304)   77 (183) 
C    90  1117 de110109r1    664 (  0)  0.14 0.14 0.00  272 (276)   49 ( 49) 
C   173  1127 ee110109r1    695 (  0)  2.78 1.51 0.00   48 (141)   45 ( 45) 
C   276  1373 ab040109r1    729 (  0)  1.66 0.83 0.00  176 (192)   81 ( 81) 
C   458  1481 dd110109f1    503 (  0)  0.91 0.18 0.00  440 (440)   36 ( 20) 
C   522  1583 dd070109r1    831 (  0)  2.11 0.10 0.90   10 ( 94)   56 ( 56) 
    539  1588 db070109r1    781 (  0)  1.09 1.74 0.00   48 ( 48)   85 (148) 
C   579  1544 eg100109f1    863 (  0)  0.32 0.53 0.21    1 ( 11)   27 ( 27) 
    850  1865 dd110109r1    516 (  0)  0.00 0.18 0.00   48 ( 48)  420 (404) 
C  1066  2097 be040109f1    732 (  0)  1.47 1.81 0.23  124 (208)   26 ( 26) 
   1240  2237 ed060109f1    888 (  0)  0.62 0.62 0.00   23 ( 23)    5 (  5) 
   1640  2596 eg020109f1    850 (  0)  0.75 0.21 0.11   21 ( 21)    1 (  1) 
C  1700  2724 da090109f1    848 (  0)  1.22 0.81 0.00   10 ( 10)   32 ( 32) 
   1884  2932 cd040109r1    835 (  0)  1.70 0.50 0.40   46 ( 46)    1 ( 62) 
   1891  2844 ed110109f1    829 (  0)  0.54 0.22 0.11   24 ( 24)    2 (  3) 
C  2126  3073 ed110109r1    804 (  0)  0.78 0.11 0.11    0 (  0)   46 ( 46) 
C  2162  3219 db070109f1    782 (  0)  1.18 1.39 0.00   93 (132)   32 ( 32) 
   2780  3804 bg020109f1    772 (  0)  0.91 1.26 0.11   32 ( 32)  117 (176) 
   3034  4045 ah070109f1    853 (  0)  1.73 0.61 0.30   28 ( 28)    0 ( 47) 
C  3141  4131 ed060109r1    893 (  0)  0.32 0.00 0.00    2 (  2)   47 ( 47) 
   3166  4224 de060109f1    823 (  0)  0.92 1.84 0.20   35 ( 35)   48 (108) 
   3379  4366 cg120109r1    826 (  0)  0.75 0.97 0.11   48 ( 48)   11 (  8) 
   3486  4457 ea060109r1    808 (  0)  1.08 1.08 0.00   46 ( 46)    0 (  6) 
   3494  4590 ab080109f1    572 (  0)  4.55 0.94 0.00  110 (110)  239 (282) 
   3535  4596 ce070109r1    833 (  0)  1.26 0.84 0.00   50 ( 50)   59 ( 59) 
C  3647  4708 cd040109f1    834 (  0)  0.71 1.42 0.30   52 (105)   26 ( 39) 
   3899  4909 dg010109f1    750 (  0)  2.72 0.22 0.76   34 ( 34)   57 ( 62) 
   3922  5104 cb040109f1    647 (  0)  3.00 1.20 0.36   88 ( 88)  263 (355) 
   4018  5141 ac050109f1    774 (  0)  2.29 0.98 0.00   88 ( 93)  119 (119) 
   4107  5119 ce110109r1    788 (  0)  0.45 1.56 0.00   53 ( 53)   64 ( 64) 
C  4145  5102 eg020109r1    824 (  0)  0.33 0.99 0.00    0 (  0)   50 ( 50) 
   4238  5288 df030109r1    786 (  0)  1.39 2.03 0.00   54 ( 54)   60 (162) 
   4468  5473 af010109f1    719 (  0)  2.52 1.49 0.34   36 ( 95)   97 (140) 
C  4570  5615 de060109r1    815 (  0)  1.20 1.41 0.00   64 ( 64)   63 ( 63) 
C  4599  5625 bg020109r1    763 (  0)  1.67 1.67 0.22   75 (163)   55 ( 55) 
C  4675  5660 cg120109f1    901 (  0)  0.73 0.31 0.10    0 (  0)   29 ( 29) 
C  4694  5735 df030109f1    826 (  0)  2.35 1.73 0.00   32 (121)   30 ( 30) 
C  4693  5803 ah070109r1    492 (  0)  2.77 1.21 0.00  486 (552)   48 ( 48) 
C  4780  5774 ce110109f1    871 (  0)  1.23 1.13 0.10    0 ( 26)   22 ( 22) 
C  4960  6060 ce070109f1    916 (  0)  1.48 0.99 0.00    4 ( 14)   82 ( 82) 
C  5045  6040 ea060109f1    729 (  0)  2.19 1.96 0.00  107 (204)   23 ( 23) 
C  5126  6160 dg010109r1    256 (  0)  13.81 1.03 0.41  504 (577)   46 (174) 
C  5553  6719 ab080109r1    316 (  0)  12.59 0.30 0.15  335 (535)  165 (220) 
   5695  6787 ae060109f1    771 (  0)  1.24 1.58 0.11   88 ( 88)  119 (208) 
C  5717  6799 cb040109r1    724 (  0)  2.68 0.93 0.12  167 (219)   57 ( 95) 
   5918  7070 cg100109r1    737 (  0)  1.66 1.18 0.00  124 (124)  185 (262) 
   6099  7135 bh080109r1    762 (  0)  2.35 1.12 0.11   62 ( 62)   81 ( 91) 
   6152  7173 be030109f1    864 (  0)  1.75 0.72 0.10   25 ( 25)   27 ( 50) 
   6186  7197 bg100109f1    830 (  0)  1.93 1.93 0.00   25 ( 25)    1 (164) 
   6321  7288 ed090109f1    865 (  0)  1.06 0.53 0.11   28 ( 28)    1 ( 33) 
   6420  7455 dg050109f1    881 (  0)  0.72 1.13 0.10   50 ( 50)   11 ( 11) 
C  6671  7862 ac050109r1    799 (  0)  1.47 0.57 0.00  145 (182)  163 (163) 
   6702  7850 de030109f1    372 (  0)  13.23 2.62 0.12   41 (182)  307 (496) 
   6712  7708 ed030109f1    634 (  0)  7.12 0.58 0.00   35 ( 35)  105 (186) 
   6938  7946 af020109f1    858 (  0)  1.58 0.32 0.11   22 ( 22)   38 ( 92) 
C  6983  7973 af010109r1     64 (  0)  16.53 1.24 0.00  353 (393)  396 (517) 
   7048  8070 dh080109f1    826 (  0)  2.74 0.81 0.10   36 ( 36)    0 ( 34) 
   7153  8212 de090109f1    863 (  0)  0.93 0.93 0.10   26 ( 26)   62 ( 84) 
C  7385  8428 ae060109r1    816 (  0)  0.89 0.78 0.00   96 ( 96)   46 ( 46) 
   7480  8549 ce080109r1     46 (  0)  26.86 0.65 0.00  531 (812)  230 (246) 
C  7523  8559 be030109r1    851 (  0)  1.55 0.93 0.10   25 (102)   45 ( 45) 
C  7736  8701 ed090109r1    808 (  0)  1.20 0.88 0.11    3 ( 45)   50 ( 47) 
   7731  8797 cg070109f1    802 (  0)  0.22 1.87 0.00   27 ( 27)  133 (161) 
   7786  8818 db060109f1    850 (  0)  2.61 0.90 0.00   26 ( 26)   12 (116) 
   7872  8921 cb030109f1    829 (  0)  1.67 0.94 0.31   26 ( 26)   67 (149) 
C  7925  8932 bh080109f1    665 (  0)  4.17 0.83 0.24  142 (235)   27 ( 27) 
C  8015  9075 dg050109r1    769 (  0)  0.23 2.08 0.00  148 (235)   46 ( 46) 
C  8065  9090 dg100109f1    823 (  0)  0.69 0.12 0.00  132 (127)   27 ( 12) 
   8148  9182 dg100109r1    807 (  0)  0.81 0.23 0.23   49 ( 44)  119 (104) 
   8156  9178 cg090109f1    867 (  0)  0.51 1.74 0.00   25 ( 25)   22 ( 74) 
C  8170  9195 bg100109r1    822 (  0)  1.95 1.74 0.10    4 ( 92)   46 ( 46) 
   8155  9154 bh120109f1    707 (  0)  2.28 2.28 0.11   30 ( 19)   94 (194) 
   8163  9188 bf120109f1    451 (  0)  5.25 0.35 0.18   22 ( 11)  433 (457) 
C  8187  9308 cg100109f1    617 (  0)  2.81 2.57 0.24  237 (237)   67 ( 67) 
   8183  9196 dc110109f1    874 (  0)  1.65 0.41 0.00   35 ( 19)   12 ( 15) 
   8195  9231 cg080109f1    862 (  0)  1.67 0.42 0.10   25 (  9)   52 ( 50) 
   8251  9313 ba040109r1     77 (  0)  22.86 0.63 0.00  405 (574)  343 (459) 
C  8292  9280 ed030109r1    539 (  0)  8.77 1.54 0.24  100 (256)   45 ( 77) 
   8338  9332 ee070109f1    902 (  0)  0.83 0.31 0.00   29 ( 29)    0 (  0) 
C  8356  9486 dc060109r1     33 (  0)  14.75 0.00 0.00  478 (498)  592 (604) 
C  8379  9425 af020109r1    190 (  0)  12.64 0.86 0.00  650 (727)   49 (125) 
C  8420  9491 de090109r1    541 (  0)  1.51 1.96 0.45   32 ( 68)  378 (378) 
C  8404  9481 de030109r1     38 (  0)  25.74 0.42 0.42  562 (668)  279 (395) 
C  8421  9485 cg090109r1    158 (  0)  23.29 0.81 0.00  303 (303)  148 (410) 
C  8437  9612 ag070109r1     52 (  0)  23.53 0.42 0.42  372 (432)  566 (620) 
C  8442  9571 ee070109r1     48 (  0)  18.75 2.40 1.92  183 (239)  739 (852) 
C  8536  9461 c03hba0049i23_t702  739 (  0)  2.06 1.26 0.11    0 (  0)   54 ( 54) 
C  8531  9460 c03hba0049i23_t701  762 (  0)  2.28 0.34 0.23    1 (  1)   53 ( 53) 
C  8546  9458 c03hba0049i23_t703  793 (  0)  1.04 0.12 0.23    0 (  0)   51 ( 51) 
   8560  9622 da010109f1    623 (  0)  4.88 0.75 0.13   32 ( 32)  232 (251) 
   8578  9585 bf020109f1    765 (  0)  0.12 0.25 0.00   29 ( 29)  178 (178) 
   8620  9626 ag110109f1    710 (  0)  0.26 0.53 0.13   29 ( 29)  219 (219) 
   8626  9601 ef100109f1    732 (  0)  0.00 0.26 0.00   20 ( 20)  194 (194) 
   8691  9708 ag070109f1    659 (  0)  0.43 0.00 0.14   23 ( 23)  301 (301) 
   8703  9764 ca060109f1    646 (  0)  0.00 0.30 0.00   31 ( 31)  357 (357) 
C  8867  9936 ce080109f1    348 (  0)  3.49 2.61 0.00   82 (160)  529 (529) 
   8865  9813 ee120109f1    498 (  0)  0.00 0.00 0.00   25 ( 25)  406 (406) 
   9177 10181 ed080109f1    188 (  0)  0.98 0.98 0.00   26 ( 26)  774 (774) 
   9183 10236 af070109f1    183 (  0)  0.51 0.51 0.51   27 ( 27)  829 (829) 

Overall discrep rates (%):             2.53 0.97 0.12

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90    6950  73.9    6950  73.9    0.00
 89      48   0.5    6998  74.4    0.00
 88      58   0.6    7056  75.0    0.00
 87      65   0.7    7121  75.7    0.00
 86      42   0.4    7163  76.1    0.00
 85      52   0.6    7215  76.7    0.00
 84      54   0.6    7269  77.3    0.00
 83      43   0.5    7312  77.7    0.00
 82      50   0.5    7362  78.3    0.00
 81     155   1.6    7517  79.9    0.00
 80      27   0.3    7544  80.2    0.00
 79      41   0.4    7585  80.6    0.00
 78      45   0.5    7630  81.1    0.00
 77      43   0.5    7673  81.6    0.00
 76      73   0.8    7746  82.3    0.00
 75      76   0.8    7822  83.2    0.00
 74      47   0.5    7869  83.7    0.00
 73      44   0.5    7913  84.1    0.00
 72      31   0.3    7944  84.4    0.00
 71      29   0.3    7973  84.8    0.00
 70      18   0.2    7991  84.9    0.00
 69      22   0.2    8013  85.2    0.00
 68      14   0.1    8027  85.3    0.00
 67      22   0.2    8049  85.6    0.00
 66     702   7.5    8751  93.0    0.00
 65      12   0.1    8763  93.2    0.00
 64      14   0.1    8777  93.3    0.00
 63      21   0.2    8798  93.5    0.00
 62      10   0.1    8808  93.6    0.00
 61     123   1.3    8931  94.9    0.00
 60      46   0.5    8977  95.4    0.00
 59       3   0.0    8980  95.5    0.00
 58       1   0.0    8981  95.5    0.00
 57       1   0.0    8982  95.5    0.00
 56      70   0.7    9052  96.2    0.00
 55       7   0.1    9059  96.3    0.00
 54      12   0.1    9071  96.4    0.00
 53      16   0.2    9087  96.6    0.00
 52      11   0.1    9098  96.7    0.00
 51      61   0.6    9159  97.4    0.00
 50       4   0.0    9163  97.4    0.00
 46       8   0.1    9171  97.5    0.00
 45      15   0.2    9186  97.7    0.00
 43       5   0.1    9191  97.7    0.00
 42      15   0.2    9206  97.9    0.00
 40      14   0.1    9220  98.0    0.00
 39       4   0.0    9224  98.1    0.01
 37       4   0.0    9228  98.1    0.01
 36       1   0.0    9229  98.1    0.01
 35       5   0.1    9234  98.2    0.01
 33       4   0.0    9238  98.2    0.01
 32       1   0.0    9239  98.2    0.01
 31       1   0.0    9240  98.2    0.01
 30       1   0.0    9241  98.2    0.01
 29      11   0.1    9252  98.4    0.03
 27       1   0.0    9253  98.4    0.03
 26       5   0.1    9258  98.4    0.04
 25       1   0.0    9259  98.4    0.04
 22       2   0.0    9261  98.4    0.06
 19       2   0.0    9263  98.5    0.08
 18       2   0.0    9265  98.5    0.11
 15       1   0.0    9266  98.5    0.14
 -1     141   1.5    9407 100.0  141.14   (quality -1 = terminal quality 0)

Avg. full length: 9407.0, trimmed (qual > -1): 9266.0
Avg. quality: 83.7 per base

Initial, terminal qual 0 segments:  1-141, (None)

Regions of LLR- adjusted quality < 2.0:
1-143, 182-184, 

3 regions, avg size 48.7, avg spacing 3135.7

First_start: 305, last_end: 9407

Slack, # used pairs (max_score), unused
 0   274  (20.4)     0 ( 0.0)      828
 1   286  (20.7)     0 ( 0.0)       88
 2   150  (19.0)     0 ( 0.0)        2
 3    65  (20.4)     0 ( 0.0)        0
 4    35  (17.6)     0 ( 0.0)        0
 5    27  (16.9)     0 ( 0.0)        0
 6    17  (18.0)     0 ( 0.0)        0
 7    16  (17.5)     0 ( 0.0)        0
 8    15  (16.8)     0 ( 0.0)        0
 9     5  (13.6)     0 ( 0.0)        0
10    11  (19.2)     0 ( 0.0)        0
11     3  (10.0)     0 ( 0.0)        0
12     3  (16.4)     0 ( 0.0)        0
13     3  (11.1)     0 ( 0.0)        0
14     1  ( 4.8)     0 ( 0.0)        0
15     2  (19.8)     0 ( 0.0)        0
16     3  (18.2)     0 ( 0.0)        0
17     2  (16.5)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 5377 -  5782      406       af010109f1   (4468)    No           1315
 9408 - right        0+      af070109f1   (9183)    No            224+

Bottom strand: 
 left -   220      220+      ec020109f1   ( 966)    Yes           966+
 6743 -  6815       73       ac050109r1   (7862)    Yes          1120 
 9408 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56  17789  17789  80618 (100.00)     6  0    0   0   0   0     0 (0.00)    0  2879 (3.57)
51   4047  21836  62829 ( 77.93)     0  0    0   0   0   0     0 (0.00)    0  2879 (4.58)
50   3170  25006  58782 ( 72.91)     0  0    0   0   0   0     0 (0.00)    0  2879 (4.90)
48    300  25306  55612 ( 68.98)     4  0    0   0   0   0     0 (0.00)    0  2879 (5.18)
47    578  25884  55312 ( 68.61)     0  0    0   0   0   0     0 (0.00)    0  2879 (5.21)
46    922  26806  54734 ( 67.89)     5  0    0   0   0   0     0 (0.00)    0  2879 (5.26)
45    760  27566  53812 ( 66.75)     0  0    0   0   0   0     0 (0.00)    0  2879 (5.35)
44   2513  30079  53052 ( 65.81)     5  0    0   0   0   0     0 (0.00)    0  2879 (5.43)
43   1724  31803  50539 ( 62.69)     1  0    0   0   0   0     0 (0.00)    0  2879 (5.70)
42   5210  37013  48815 ( 60.55)    11  0    0   0   0   0     0 (0.00)    0  2879 (5.90)
41    479  37492  43605 ( 54.09)     0  0    0   0   0   0     0 (0.00)    0  2879 (6.60)
40   3195  40687  43126 ( 53.49)    14  0    0   0   0   0     0 (0.00)    0  2879 (6.68)
39    195  40882  39931 ( 49.53)     2  0    0   0   0   0     0 (0.00)    0  2879 (7.21)
38    306  41188  39736 ( 49.29)     0  0    0   0   0   0     0 (0.00)    0  2879 (7.25)
37   1732  42920  39430 ( 48.91)     8  0    0   0   0   0     0 (0.00)    0  2879 (7.30)
36    219  43139  37698 ( 46.76)     2  0    0   0   0   0     0 (0.00)    0  2879 (7.64)
35   1512  44651  37479 ( 46.49)     2  0    0   0   2   0     2 (0.13)    2  2879 (7.68)
34    598  45249  35967 ( 44.61)     1  0    0   0   0   1     1 (0.17)    3  2877 (8.00)
33   1112  46361  35369 ( 43.87)    14  0    0   0   0   0     0 (0.00)    3  2876 (8.13)
32    826  47187  34257 ( 42.49)     8  0    0   0   0   0     0 (0.00)    3  2876 (8.40)
31    478  47665  33431 ( 41.47)     5  0    0   0   0   0     0 (0.00)    3  2876 (8.60)
30    535  48200  32953 ( 40.88)     6  0    0   0   0   0     0 (0.00)    3  2876 (8.73)
29   1592  49792  32418 ( 40.21)    35  0    0   0   3   1     4 (0.25)    7  2876 (8.87)
28    481  50273  30826 ( 38.24)     6  0    0   0   1   0     1 (0.21)    8  2872 (9.32)
27    798  51071  30345 ( 37.64)     9  0    0   0   1   0     1 (0.13)    9  2871 (9.46)
26    386  51457  29547 ( 36.65)     3  0    0   0   0   0     0 (0.00)    9  2870 (9.71)
25    919  52376  29161 ( 36.17)    19  0    0   0   2   0     2 (0.22)   11  2870 (9.84)
24    792  53168  28242 ( 35.03)    12  0    0   1   1   1     3 (0.38)   14  2868 (10.16)
23    729  53897  27450 ( 34.05)    28  0    0   4   1   0     5 (0.69)   19  2865 (10.44)
22    666  54563  26721 ( 33.15)    21  0    0   3   2   1     6 (0.90)   25  2860 (10.70)
21    847  55410  26055 ( 32.32)    23  0    0   7   4   0    11 (1.30)   36  2854 (10.95)
20    649  56059  25208 ( 31.27)    35  0    0   4   1   0     5 (0.77)   41  2843 (11.28)
19   1113  57172  24559 ( 30.46)    54  0    0  10   3   0    13 (1.17)   54  2838 (11.56)
18    765  57937  23446 ( 29.08)    34  0    0  14   6   0    20 (2.61)   74  2825 (12.05)
17    832  58769  22681 ( 28.13)    49  0    0  17   4   0    21 (2.52)   95  2805 (12.37)
16    967  59736  21849 ( 27.10)    63  0    0  16  10   3    29 (3.00)  124  2784 (12.74)
15   1205  60941  20882 ( 25.90)    71  0    0  29   8   2    39 (3.24)  163  2755 (13.19)
14   1124  62065  19677 ( 24.41)    78  0    0  54  13   0    67 (5.96)  230  2716 (13.80)
13   1533  63598  18553 ( 23.01)   127  0    0  69  19   1    89 (5.81)  319  2649 (14.28)
12   1477  65075  17020 ( 21.11)   104  0    0  82  23   4   109 (7.38)  428  2560 (15.04)
11   2579  67654  15543 ( 19.28)   197  0    0 240  36  12   288 (11.17)  716  2451 (15.77)
10   2749  70403  12964 ( 16.08)   211  0    0 256  61  10   327 (11.90)  1043  2163 (16.68)
 9   4142  74545  10215 ( 12.67)   466  0    0 376 124  38   538 (12.99)  1581  1836 (17.97)
 8   2664  77209   6073 (  7.53)   347  0    0 318 149  10   477 (17.91)  2058  1298 (21.37)
 7   2121  79330   3409 (  4.23)   181  0    0 301 146   7   454 (21.40)  2512  821 (24.08)
 6   1130  80460   1288 (  1.60)   212  0    0 173 121   3   297 (26.28)  2809  367 (28.49)
 4    140  80600    158 (  0.20)   126  0    0  42   8   2    52 (37.14)  2861   70 (44.30)
 0     18  80618     18 (  0.02)    41  0   12   0   6   0    18 (100.00)  2879   18 (100.00)
-1    159  80777      0 (  0.00)  16033  0    0   0   2   0     2 (1.26)  2881    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90  51694  51694  74919 (100.00)     0  0    0   0   0   0     0 (0.00)    0  1582 (2.11)
89    231  51925  23225 ( 31.00)     0  0    0   0   0   0     0 (0.00)    0  1582 (6.81)
88    289  52214  22994 ( 30.69)     0  0    0   0   0   0     0 (0.00)    0  1582 (6.88)
87    319  52533  22705 ( 30.31)     0  0    0   0   0   0     0 (0.00)    0  1582 (6.97)
86    160  52693  22386 ( 29.88)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.07)
85    220  52913  22226 ( 29.67)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.12)
84    185  53098  22006 ( 29.37)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.19)
83    154  53252  21821 ( 29.13)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.25)
82    185  53437  21667 ( 28.92)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.30)
81    634  54071  21482 ( 28.67)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.36)
80     69  54140  20848 ( 27.83)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.59)
79     99  54239  20779 ( 27.74)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.61)
78    137  54376  20680 ( 27.60)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.65)
77     95  54471  20543 ( 27.42)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.70)
76    192  54663  20448 ( 27.29)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.74)
75    169  54832  20256 ( 27.04)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.81)
74    111  54943  20087 ( 26.81)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.88)
73     97  55040  19976 ( 26.66)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.92)
72     65  55105  19879 ( 26.53)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.96)
71     94  55199  19814 ( 26.45)     0  0    0   0   0   0     0 (0.00)    0  1582 (7.98)
70     38  55237  19720 ( 26.32)     0  0    0   0   0   0     0 (0.00)    0  1582 (8.02)
69     65  55302  19682 ( 26.27)     0  0    0   0   0   0     0 (0.00)    0  1582 (8.04)
68     31  55333  19617 ( 26.18)     0  0    0   0   0   0     0 (0.00)    0  1582 (8.06)
67     72  55405  19586 ( 26.14)     0  0    0   0   0   0     0 (0.00)    0  1582 (8.08)
66   5034  60439  19514 ( 26.05)     0  0    0   0   0   0     0 (0.00)    0  1582 (8.11)
65    156  60595  14480 ( 19.33)     0  0    0   0   0   0     0 (0.00)    0  1582 (10.93)
64     38  60633  14324 ( 19.12)     0  0    0   0   0   0     0 (0.00)    0  1582 (11.04)
63     28  60661  14286 ( 19.07)     0  0    0   0   0   0     0 (0.00)    0  1582 (11.07)
62     52  60713  14258 ( 19.03)     0  0    0   0   0   0     0 (0.00)    0  1582 (11.10)
61    722  61435  14206 ( 18.96)     0  0    0   0   0   0     0 (0.00)    0  1582 (11.14)
60    290  61725  13484 ( 18.00)     0  0    0   0   0   0     0 (0.00)    0  1582 (11.73)
59     52  61777  13194 ( 17.61)     0  0    0   0   0   0     0 (0.00)    0  1582 (11.99)
58     75  61852  13142 ( 17.54)     0  0    0   0   0   0     0 (0.00)    0  1582 (12.04)
57    111  61963  13067 ( 17.44)     0  0    0   0   0   0     0 (0.00)    0  1582 (12.11)
56    275  62238  12956 ( 17.29)     0  0    0   0   0   0     0 (0.00)    0  1582 (12.21)
55     53  62291  12681 ( 16.93)     0  0    0   0   0   0     0 (0.00)    0  1582 (12.48)
54    259  62550  12628 ( 16.86)     0  0    0   0   0   0     0 (0.00)    0  1582 (12.53)
53    134  62684  12369 ( 16.51)     0  0    0   0   0   0     0 (0.00)    0  1582 (12.79)
52    282  62966  12235 ( 16.33)     0  0    0   0   0   0     0 (0.00)    0  1582 (12.93)
51    103  63069  11953 ( 15.95)     0  0    0   0   0   0     0 (0.00)    0  1582 (13.24)
50    103  63172  11850 ( 15.82)     0  0    0   0   0   0     0 (0.00)    0  1582 (13.35)
49     89  63261  11747 ( 15.68)     0  0    0   0   0   0     0 (0.00)    0  1582 (13.47)
48     70  63331  11658 ( 15.56)     0  0    0   0   0   0     0 (0.00)    0  1582 (13.57)
47     63  63394  11588 ( 15.47)     0  0    0   0   0   0     0 (0.00)    0  1582 (13.65)
46    114  63508  11525 ( 15.38)     0  0    0   0   0   0     0 (0.00)    0  1582 (13.73)
45     97  63605  11411 ( 15.23)     0  0    0   0   0   0     0 (0.00)    0  1582 (13.86)
44    131  63736  11314 ( 15.10)     1  0    0   0   0   0     0 (0.00)    0  1582 (13.98)
43     99  63835  11183 ( 14.93)     0  0    0   0   0   0     0 (0.00)    0  1582 (14.15)
42    151  63986  11084 ( 14.79)     3  0    0   0   0   0     0 (0.00)    0  1582 (14.27)
41    139  64125  10933 ( 14.59)     0  0    0   0   0   0     0 (0.00)    0  1582 (14.47)
40   2163  66288  10794 ( 14.41)     3  0    0   0   0   0     0 (0.00)    0  1582 (14.66)
39     31  66319   8631 ( 11.52)     0  0    0   0   0   0     0 (0.00)    0  1582 (18.33)
38     24  66343   8600 ( 11.48)     1  0    0   0   0   0     0 (0.00)    0  1582 (18.40)
37     52  66395   8576 ( 11.45)     3  0    0   0   0   0     0 (0.00)    0  1582 (18.45)
36     40  66435   8524 ( 11.38)     1  0    0   0   0   0     0 (0.00)    0  1582 (18.56)
35     61  66496   8484 ( 11.32)     0  0    0   0   1   0     1 (1.64)    1  1582 (18.65)
34     81  66577   8423 ( 11.24)     0  0    0   0   1   1     2 (2.47)    3  1581 (18.77)
33     91  66668   8342 ( 11.13)     4  0    0   0   1   0     1 (1.10)    4  1579 (18.93)
32     57  66725   8251 ( 11.01)     1  0    0   0   0   0     0 (0.00)    4  1578 (19.12)
31     51  66776   8194 ( 10.94)     1  0    0   0   0   0     0 (0.00)    4  1578 (19.26)
30     32  66808   8143 ( 10.87)     1  0    0   0   0   0     0 (0.00)    4  1578 (19.38)
29     96  66904   8111 ( 10.83)     4  0    0   0   3   1     4 (4.17)    8  1578 (19.46)
28     28  66932   8015 ( 10.70)     0  0    0   0   1   0     1 (3.57)    9  1574 (19.64)
27     53  66985   7987 ( 10.66)     0  0    0   0   1   0     1 (1.89)   10  1573 (19.69)
26     71  67056   7934 ( 10.59)     1  0    0   0   0   0     0 (0.00)   10  1572 (19.81)
25    387  67443   7863 ( 10.50)     2  0    0   4   2   1     7 (1.81)   17  1572 (19.99)
24     98  67541   7476 (  9.98)     3  0    0   0   1   1     2 (2.04)   19  1565 (20.93)
23     86  67627   7378 (  9.85)     2  0    0   6   2   0     8 (9.30)   27  1563 (21.18)
22     71  67698   7292 (  9.73)     0  0    0   4   2   1     7 (9.86)   34  1555 (21.32)
21     81  67779   7221 (  9.64)     0  0    0   5   4   0     9 (11.11)   43  1548 (21.44)
20     71  67850   7140 (  9.53)     1  0    0   1   1   0     2 (2.82)   45  1539 (21.55)
19    154  68004   7069 (  9.44)     0  0    0   8   3   0    11 (7.14)   56  1537 (21.74)
18     83  68087   6915 (  9.23)     1  0    0   6   5   0    11 (13.25)   67  1526 (22.07)
17    113  68200   6832 (  9.12)     3  0    0   8   3   0    11 (9.73)   78  1515 (22.18)
16    189  68389   6719 (  8.97)     4  0    0   9   7   2    18 (9.52)   96  1504 (22.38)
15    203  68592   6530 (  8.72)     5  0    0  15   6   2    23 (11.33)  119  1486 (22.76)
14    238  68830   6327 (  8.45)     5  0    0  25   9   0    34 (14.29)  153  1463 (23.12)
13    398  69228   6089 (  8.13)     4  0    0  32  11   1    44 (11.06)  197  1429 (23.47)
12    363  69591   5691 (  7.60)     3  0    0  39  13   3    55 (15.15)  252  1385 (24.34)
11    720  70311   5328 (  7.11)     3  0    0 113  21   9   143 (19.86)  395  1330 (24.96)
10    872  71183   4608 (  6.15)     5  0    0 151  29  10   190 (21.79)  585  1187 (25.76)
 9   1371  72554   3736 (  4.99)     4  0    0 159  66  31   256 (18.67)  841  997 (26.69)
 8    969  73523   2365 (  3.16)    14  0    0 171  84   6   261 (26.93)  1102  741 (31.33)
 7    856  74379   1396 (  1.86)     7  0    0 188  95   3   286 (33.41)  1388  480 (34.38)
 6    453  74832    540 (  0.72)     0  0    0 105  52   3   160 (35.32)  1548  194 (35.93)
 4     80  74912     87 (  0.12)     0  0    0  18   8   1    27 (33.75)  1575   34 (39.08)
 0      7  74919      7 (  0.01)     0  0    1   0   6   0     7 (100.00)  1582    7 (100.00)
-1   5858  80777      0 (  0.00)  18589  0   11 949 319  20   1299 (22.17)  2881    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     141      141        1
 15       1      142        1
 18       2      144        2
 19       2      146        2
 22       2      148        2
 25       1      149        2
 26       5      154        3
 27       1      155        3
 29      11      166        5
 30       1      167        5
 31       1      168        5
 32       1      169        6
 33       4      173        4
 35       5      178        4
 36       1      179        4
 37       4      183        5
 39       4      187        4
 40      14      201        7
 42      15      216        9
 43       5      221       12
 45      15      236       11
 46       8      244       12
 50       4      248       13
 51      61      309       14
 52      11      320       23
 53      16      336       30
 54      12      348       36
 55       7      355       38
 56      70      425       31
 57       1      426       31
 58       1      427       31
 59       3      430       33
 60      46      476       52
 61     123      599       70
 62      10      609       74
 63      21      630       76
 64      14      644       81
 65      12      656       88
 66     702     1358       58
 67      22     1380       64
 68      14     1394       63
 69      22     1416       64
 70      18     1434       68
 71      29     1463       71
 72      31     1494       71
 73      44     1538       90
 74      47     1585       98
 75      76     1661      108
 76      73     1734      114
 77      43     1777      110
 78      45     1822      116
 79      41     1863      113
 80      27     1890      107
 81     155     2045      121
 82      50     2095      114
 83      43     2138      116
 84      54     2192      115
 85      52     2244      116
 86      42     2286      119
 87      65     2351      127
 88      58     2409      134
 89      48     2457      136
 90    6950     9407        1

SS region: 699 (7.43%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
 1446     -4.4  [-4.4,  0.0]  (1, 0)
 4085     -5.6  [-5.6,  0.0]  (0, 1)
 5801     -3.4  [-3.4,  0.0]  (1, 0)
 8800     -3.5  [-3.5,  0.0]  (0, 1)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)   283-  941 [13.0] (0,0)   C ec020109f1         683-26 | 26 683  (739 887) | DA:(739 887) CHIMERIC || local(+/-) (14.1,0.0), distant (2.8,0.0)
(0, 0)   452- 1292 [16.4] (0,0)   C ab040109r1         929-82 | (5 86)  82 930 | DU:(5 81) [5 86  with   ah100109r1  66 146]  CHIMERIC || local(+/-) (14.6,0.0), distant (0.0,0.0)
(0, 0)  5630- 6114 [ 2.8] (0,0)   C dg010109r1         534-47 | (16 50)  47 534 | DU:(16 46) [16 50  with   ae120109r1  114 149]  CHIMERIC || local(+/-) (6.7,0.0), distant (0.0,0.0)
(0, 0)  6816- 7699 [16.1] (0,0)   C ac050109r1         1052-164 | (99 163)  164 1074 | DU:(99 163) [99 163  with   ba120109r1  0 61]  CHIMERIC || local(+/-) (16.2,11.0), distant (0.0,0.0)
(0, 0)  6743- 7543 [-2.5] (0,0)     de030109f1         42-862 || local(+/-) (11.7,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -12.3 (<20 part: -12.3 (#=128), >20:0.0 (#=0); in HQ: -2.4, out HQ -9.9), match: 9.7  trail: 0.0  lead: 0.0  total: -2.6 
(274, 0)  8656- 8970 [ 0.5] (0,0)     ba040109r1         406-722 || local(+/-) (5.4,0.0), distant (0.0,0.0)
(0, 0)  8966- 9202 [-3.6] (0,0)   C de030109r1         516-280 || local(+/-) (3.9,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -5.1 (<20 part: -5.1 (#=63), >20:0.0 (#=0); in HQ: 0.0, out HQ -5.1), match: 1.5  trail: 0.0  lead: 0.0  total: -3.6 
(0, 0)  8724- 9337 [-6.7] (0,0)   C cg090109r1         767-149 || local(+/-) (4.2,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -13.1 (<20 part: -13.1 (#=148), >20:0.0 (#=0); in HQ: -3.3, out HQ -9.8), match: 6.3  trail: 0.0  lead: 0.0  total: -6.8 
(0, 0)  8809- 9046 [-1.5] (0,0)   C ag070109r1         804-567 || local(+/-) (4.9,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -4.4 (<20 part: -4.4 (#=58), >20:0.0 (#=0); in HQ: 0.0, out HQ -4.4), match: 2.9  trail: 0.0  lead: 0.0  total: -1.5 

Gaps in unique-read coverage:  None.

Contig 16.  137 reads; 11560 bp (untrimmed), 11524 (trimmed).
    -47   921 eb100109r1    838 (  0)  0.88 0.00 0.11   48 (164)    8 (  8) 
     31  1133 ad060109f1    860 (  0)  2.06 0.79 0.20   86 ( 86)    0 (135) 
C   536  1478 eh020109r1    836 (  0)  0.34 0.11 0.00    0 (  0)   49 (474) 
C   992  2027 dd020109r1    812 (  0)  0.96 1.06 0.00   43 (575)   52 ( 52) 
   1518  2628 cc080109f1    741 (  0)  1.63 1.31 0.11   52 ( 43)  140 (124) 
   1533  2543 eb040109f1    869 (  0)  0.62 0.10 0.00   24 ( 24)   14 ( 10) 
   1542  2578 ac080109f1    822 (  0)  1.69 1.09 0.10   28 (  8)    2 ( 44) 
   1546  2586 cf090109f1    790 (  0)  0.55 0.44 0.11   24 (  7)  115 ( 78) 
   1585  2606 bf100109r1    802 (  0)  1.23 1.03 0.10   44 ( 44)    6 ( 57) 
C  1600  2565 eb100109f1    839 (  0)  0.32 0.32 0.00    0 (  0)   23 ( 23) 
   1771  2766 bg090109f1    766 (  0)  1.98 0.94 0.10   31 ( 31)    3 ( 84) 
   1818  2865 df100109r1    747 (  0)  0.99 1.32 0.00   47 ( 47)   89 (128) 
C  1828  2883 cf040109f1    503 (  0)  0.53 0.18 0.00  448 (448)   37 ( 25) 
   1826  2961 ad120109f1    729 (  0)  0.80 0.69 0.23  157 (157)  107 (129) 
   1918  2914 ag020109f1    828 (  0)  0.93 0.42 0.00   26 ( 26)    8 (  8) 
   2109  3111 dd120109f1    799 (  0)  1.04 1.66 0.00   32 ( 36)    5 ( 66) 
   2227  3280 cf040109r1    507 (  0)  0.35 0.17 0.00   49 ( 49)  430 (421) 
   2518  3552 ca040109r1    793 (  0)  2.55 0.41 0.41   50 ( 50)    3 (  3) 
C  2686  3719 cg050109f1    548 (  0)  0.17 0.00 0.00  405 (405)   33 ( 17) 
   2874  3879 ah020109f1    737 (  0)  1.00 1.88 0.00   29 ( 29)   75 (118) 
   2914  3920 ca020109r1    766 (  0)  2.10 0.42 0.53   50 ( 50)    5 ( 20) 
C  2971  4024 ad060109r1    790 (  0)  1.81 1.61 0.10   10 ( 10)   48 ( 48) 
C  2972  3984 bf100109f1    762 (  0)  2.01 1.06 0.11   45 (110)   21 ( 21) 
   3045  4075 cg050109r1    546 (  0)  0.17 0.00 0.00   46 ( 46)  389 (373) 
   3165  4136 ef030109r1    824 (  0)  1.08 0.00 0.11   44 ( 44)    0 (  0) 
C  3315  4389 cc080109r1    731 (  0)  0.57 1.58 0.00  135 (145)   56 ( 21) 
C  3339  4382 ac080109r1    808 (  0)  1.91 0.81 0.30    2 ( 60)   49 ( 18) 
C  3368  4380 cf090109r1    800 (  0)  1.45 0.83 0.10    3 ( 31)   47 ( 14) 
   3382  4463 da040109r1    718 ( 33)  0.47 1.63 0.00   50 ( 50)  174 (203) 
C  3435  4439 eb040109r1    851 ( 86)  0.62 0.21 0.00    0 (  5)   45 ( 45) 
C  3497  4503 ag020109r1    811 (140)  1.04 0.73 0.00    0 ( 48)   50 ( 50) 
C  3537  4626 ad120109r1    754 (179)  1.53 1.20 0.00   53 ( 76)  122 (122) 
   3643  4830 aa050109r1    697 (241)  2.24 1.90 0.00  177 (177)  117 (239) 
   3821  4968 cb050109r1    730 (202)  1.38 1.15 0.11   98 ( 98)  179 (179) 
   3999  5105 dd040109f1    740 (346)  1.63 1.63 0.00   34 ( 34)  154 (181) 
C  4028  5070 ca040109f1    690 (346)  1.48 3.48 0.21   70 ( 78)   25 ( 25) 
C  4109  5115 dd120109r1    750 (311)  0.76 1.85 0.00   42 ( 69)   48 ( 48) 
   4252  5314 ca090109f1    768 (263)  0.44 1.22 0.11   28 ( 28)  130 (113) 
C  4259  5512 bg090109r1    279 (  0)  3.63 0.00 0.00  850 (895)   46 ( 46) 
   4272  5311 bf050109r1    721 (232)  1.66 2.91 0.10   50 ( 50)   29 (112) 
   4299  5381 bc040109f1    760 (229)  0.23 1.03 0.11   25 ( 25)  183 (176) 
C  4330  5378 ah020109r1     39 (  0)  16.52 0.00 0.87  888 (888)   46 (124) 
   4450  5632 dd060109f1    673 (241)  3.20 1.65 0.00  105 (105)  171 (272) 
   4955  6001 be050109r1    755 (  0)  2.41 1.61 0.10   47 ( 47)    4 ( 92) 
   4990  6022 dd090109r1    748 (  0)  2.38 1.34 0.00   48 ( 46)   17 ( 80) 
C  5016  6088 da040109f1    682 (  0)  1.69 0.48 0.12  202 (207)   42 ( 42) 
C  5021  6046 ca020109f1    673 (  0)  0.88 0.38 0.13  195 (195)   36 ( 36) 
C  5180  6235 df100109f1    760 (  0)  0.88 0.99 0.00  119 (145)   31 ( 31) 
C  5227  6273 bf090109r1    639 (  0)  2.74 1.82 0.11  109 (190)   61 ( 61) 
   5244  6245 bf090109f1    649 (  0)  4.36 1.91 0.11   26 ( 26)   35 (239) 
C  5500  6620 dd040109r1    703 (  0)  0.00 1.67 0.00  232 (260)   49 ( 49) 
C  5522  6550 be050109f1    797 (  0)  1.25 1.15 0.00   43 ( 73)   26 ( 26) 
C  5694  6763 dd060109r1    768 (  0)  1.68 1.26 0.00   66 ( 93)   52 ( 52) 
C  5730  6725 ch010109f1    667 (  0)  0.92 0.26 0.00  198 (192)   36 ( 36) 
C  5835  6879 bc040109r1    824 (  0)  1.52 0.20 0.41    9 ( 17)   50 ( 50) 
   5876  6894 ch010109r1    655 (  0)  0.79 0.52 0.13   52 ( 46)  205 (226) 
C  5963  7150 aa050109f1    765 (  0)  0.89 1.33 0.00  119 (119)  170 (177) 
   5978  7083 bb080109r1      4 (  0)  0.00 0.00 0.00   13 ( 49) 1085 (1026) 
   5982  6997 eg050109r1      8 (  0)  0.00 0.00 0.00  894 (  9)  114 (964) 
   6032  7042 ch080109r1    810 (  0)  1.15 1.15 0.10   51 ( 51)    0 ( 88) 
   6050  7090 bd010109r1      7 (  0)  10.00 0.00 0.00  932 ( 18)   99 (992) 
   6031  7088 ac030109r1      3 (  0)  0.00 0.00 0.00 1020 (  8)   32 (1009) 
C  6100  7162 cb020109f1    774 (  0)  0.36 0.12 0.12  195 (186)   25 ( 25) 
C  6176  7189 bf050109f1    801 (  0)  2.07 1.04 0.00   22 ( 97)   27 ( 27) 
   6184  7214 dg040109f1    829 (  0)  1.11 1.51 0.10   28 ( 28)    9 ( 61) 
   6246  7292 cb020109r1    734 (  0)  0.60 0.96 0.00   49 ( 41)  166 (166) 
C  6498  7544 dd090109f1    804 (  0)  1.05 1.78 0.00   64 ( 69)   28 ( 28) 
   6562  7623 cf080109r1    849 (  0)  1.62 0.91 0.00   52 ( 52)   24 ( 39) 
   6571  7579 ah040109r1    820 (  0)  1.46 1.25 0.00   43 ( 43)    7 ( 38) 
   6674  7701 bc050109f1    780 (  0)  2.01 1.69 0.00   25 ( 25)   57 (122) 
C  6731  7850 ca090109r1    823 (  0)  0.87 0.98 0.00   68 ( 98)  131 (131) 
   6809  7839 be060109r1    862 (  0)  0.72 1.14 0.00   47 ( 47)   18 ( 40) 
   6996  8012 de100109r1    870 (  0)  1.55 0.21 0.21   46 ( 46)    3 ( 57) 
C  7028  8010 ef030109f1    880 (  0)  0.84 0.31 0.10    0 (  4)   27 ( 27) 
   7106  8070 ec100109r1    842 (  0)  0.98 0.11 0.11   46 ( 46)    5 ( 28) 
   7363  8378 ah120109r1    787 (  0)  0.69 1.03 0.00   64 ( 64)   81 ( 81) 
   7365  8398 dg030109f1    857 (  0)  1.23 1.43 0.00   29 ( 29)   26 (105) 
   7375  8467 da030109r1    611 (  0)  3.20 1.33 0.00   53 ( 53)  289 (289) 
   7547  8644 db090109r1    552 (  0)  5.65 0.27 0.27  134 (174)  220 (287) 
   7787  8880 ac090109r1    711 (  0)  0.62 1.37 0.00   47 ( 47)  245 (245) 
C  7806  8773 ec100109f1    881 ( 49)  0.53 0.21 0.11    0 (  0)   21 ( 21) 
C  8027  9036 ch080109f1    883 (  0)  1.02 0.20 0.31    6 ( 10)   26 ( 26) 
C  8123  9169 bc050109r1    866 (  0)  2.21 0.20 0.30    2 ( 81)   48 ( 48) 
C  8136  9158 be060109f1    845 (  0)  0.65 0.75 0.00   70 ( 70)   24 ( 24) 
C  8222  9287 cf080109f1    852 (  0)  0.84 1.15 0.00   82 ( 87)   27 (  9) 
C  8281  9283 ah040109f1    823 (  0)  1.95 1.13 0.31    4 ( 44)   25 (  6) 
C  8349  9368 dg040109r1    824 (  0)  2.06 1.14 0.10    4 (101)   47 ( 47) 
   8370  9322 ee010109r1    836 (  0)  0.78 0.11 0.22   50 ( 50)    0 ( 22) 
   8394  9449 bb020109f1    598 (  0)  5.89 1.68 0.00  124 (135)  100 (154) 
   8419  9418 aa110109f1    817 (  0)  2.05 0.22 0.22   19 ( 26)   56 ( 56) 
C  8655  9679 de100109f1    908 (  0)  1.31 0.40 0.00    1 ( 24)   34 ( 34) 
   8680  9629 ed120109r1    825 (  0)  1.33 0.33 0.11   48 ( 48)    2 (  9) 
   8871  9921 ch050109f1    813 (  0)  0.57 0.79 0.11   31 ( 31)  139 (139) 
C  8912 10115 db090109f1    473 (  0)  8.39 0.43 0.14  385 (543)  128 (145) 
   8915 10106 ae090109f1    806 (  0)  1.95 1.09 0.00  154 (154)  117 (159) 
   9022 10170 cc060109r1    748 (  0)  2.72 0.91 0.23  115 (115)  152 (189) 
   9052 10172 aa080109f1    828 (  0)  1.79 1.16 0.11  139 (139)   34 ( 83) 
C  9056 10013 ea100109r1    587 (  0)  0.49 0.33 0.00  299 (284)   46 ( 46) 
C  9096 10126 dg030109r1    819 (  0)  1.23 0.56 0.11   93 (131)   46 ( 46) 
   9219 10212 ec030109r1    823 (  0)  0.45 1.23 0.00   49 ( 49)   48 ( 78) 
C  9227 10222 ah120109f1    813 (  0)  2.11 1.05 0.32   16 ( 85)   31 ( 31) 
   9321 10368 cd030109f1    858 (  0)  1.54 1.33 0.00   34 ( 32)   40 (107) 
   9328 10284 ea100109f1    596 (  0)  0.16 0.00 0.16   27 ( 12)  317 (317) 
C  9463 10448 ec030109f1    870 (  0)  0.73 1.15 0.00    5 (  5)   27 ( 98) 
C  9618 10847 ae090109r1    723 (  0)  2.10 0.49 0.00  211 (232)  208 (237) 
   9816 10950 cd080109f1    733 (  0)  2.94 1.36 0.00   80 ( 80)  171 (214) 
C  9831 10864 ad010109r1     33 (  0)  10.34 0.00 1.72  915 (915)   61 ( 61) 
   9858 11031 ah080109f1    368 (  0)  9.36 1.48 0.33  393 (393)  172 (321) 
   9887 10937 db020109f1    791 (  0)  2.03 1.82 0.00   38 ( 38)   78 (135) 
  10016 11029 ah060109f1    835 (  0)  1.27 1.38 0.00   24 ( 24)   47 (107) 
C 10061 11010 ee010109f1    844 (  0)  0.65 0.97 0.22    0 (  0)   22 ( 22) 
  10071 11116 af050109f1    821 (  0)  0.54 1.63 0.11   27 ( 27)   99 ( 98) 
C 10296 11366 da030109f1    529 (  0)  8.63 0.76 0.25  230 (230)   53 ( 98) 
  10301 11432 ce030109f1    818 (  0)  1.11 1.00 0.00   74 ( 74)  155 (183) 
C 10333 11447 ac090109f1    879 (  0)  1.44 0.51 0.21   12 ( 43)  130 (130) 
C 10354 11409 bb020109r1    610 (  0)  6.15 1.00 0.00  208 (231)   51 ( 96) 
C 10416 11407 aa110109r1    825 (  0)  1.62 0.86 0.11   19 ( 67)   47 ( 47) 
  10519 11502 eg060109f1    870 (  0)  0.73 1.35 0.00   23 ( 23)    0 ( 54) 
C 10556 11509 ed120109f1    871 (  0)  0.54 0.43 0.00    0 (  0)   33 ( 33) 
C 10592 11564 c03hba0049i23_sp601  656 (  0)  2.70 1.03 0.26  186 (230)    8 (  7) 
  10598 11576 be120109f1    855 (  0)  1.49 0.32 0.21   23 ( 22)   16 ( 16) 
C 10614 11754 cc060109f1    654 (  0)  1.32 1.84 0.00  188 (222)  194 (194) 
C 10605 11567 c03hba0049i23_sp602  705 (  0)  1.41 0.77 0.00  173 (184)    9 (  9) 
C 10610 11565 c03hba0049i23_sp603  695 (  0)  1.31 0.39 0.26  182 (178)    9 (  8) 
C 10690 11722 cd030109r1    741 (  0)  2.31 1.27 0.00    5 ( 75)  162 (162) 
  10712 11754 ad010109f1     44 (  0)  0.00 1.96 0.00   35 ( 35)  957 (957) 
C 10852 11871 ch050109r1    548 (  0)  1.49 2.84 0.00   40 ( 58)  311 (311) 
  10880 11921 bb090109f1    599 (  0)  1.39 0.31 0.00   32 ( 32)  361 (361) 
  10927 11960 ba080109f1    524 (  0)  1.03 1.03 0.00   51 ( 44)  403 (403) 
  11147 12202 ed020109f1    368 (  0)  0.77 0.00 0.00   25 ( 25)  642 (642) 
  11163 12286 ef060109f1    346 (  0)  1.35 0.00 0.00   27 ( 27)  726 (726) 
  11190 12273 aa120109f1    202 (  0)  8.23 1.90 0.00   55 (119)  713 (713) 
  11250 12415 bf060109f1    217 (  0)  3.53 2.47 0.00   28 ( 36)  855 (855) 
  11244 12281 da110109f1    247 (  0)  2.44 0.70 0.35   30 ( 30)  721 (721) 
  11261 12312 ef080109f1    251 (  0)  1.12 0.00 0.00   33 ( 33)  752 (752) 
  11326 12342 be110109r1    178 (  0)  1.07 0.00 0.00   48 ( 48)  782 (782) 
  11425 12524 ac060109r1     75 (  0)  2.33 1.16 0.00   50 ( 50)  964 (964) 

Overall discrep rates (%):             1.63 0.97 0.09

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90    9317  80.6    9317  80.6    0.00
 89      27   0.2    9344  80.8    0.00
 88      29   0.3    9373  81.1    0.00
 87      12   0.1    9385  81.2    0.00
 86      13   0.1    9398  81.3    0.00
 85      22   0.2    9420  81.5    0.00
 84      17   0.1    9437  81.6    0.00
 83      18   0.2    9455  81.8    0.00
 82      18   0.2    9473  81.9    0.00
 81     104   0.9    9577  82.8    0.00
 80      11   0.1    9588  82.9    0.00
 79      25   0.2    9613  83.2    0.00
 78      17   0.1    9630  83.3    0.00
 77      23   0.2    9653  83.5    0.00
 76      35   0.3    9688  83.8    0.00
 75      33   0.3    9721  84.1    0.00
 74      21   0.2    9742  84.3    0.00
 73      20   0.2    9762  84.4    0.00
 72      15   0.1    9777  84.6    0.00
 71      39   0.3    9816  84.9    0.00
 70      10   0.1    9826  85.0    0.00
 69      30   0.3    9856  85.3    0.00
 68      18   0.2    9874  85.4    0.00
 67      22   0.2    9896  85.6    0.00
 66     701   6.1   10597  91.7    0.00
 65       8   0.1   10605  91.7    0.00
 64       5   0.0   10610  91.8    0.00
 63      10   0.1   10620  91.9    0.00
 62      11   0.1   10631  92.0    0.00
 61     190   1.6   10821  93.6    0.00
 60      37   0.3   10858  93.9    0.00
 59       3   0.0   10861  94.0    0.00
 58       7   0.1   10868  94.0    0.00
 57      12   0.1   10880  94.1    0.00
 56     362   3.1   11242  97.2    0.00
 55      19   0.2   11261  97.4    0.00
 54      17   0.1   11278  97.6    0.00
 53      18   0.2   11296  97.7    0.00
 52      38   0.3   11334  98.0    0.00
 51      84   0.7   11418  98.8    0.00
 50      29   0.3   11447  99.0    0.00
 49       2   0.0   11449  99.0    0.00
 48       4   0.0   11453  99.1    0.00
 47       5   0.0   11458  99.1    0.00
 46       9   0.1   11467  99.2    0.00
 45       1   0.0   11468  99.2    0.00
 44       5   0.0   11473  99.2    0.00
 43       8   0.1   11481  99.3    0.00
 42       9   0.1   11490  99.4    0.00
 40      13   0.1   11503  99.5    0.01
 39       1   0.0   11504  99.5    0.01
 37       2   0.0   11506  99.5    0.01
 35       5   0.0   11511  99.6    0.01
 33       1   0.0   11512  99.6    0.01
 30       2   0.0   11514  99.6    0.01
 29       1   0.0   11515  99.6    0.01
 28       4   0.0   11519  99.6    0.02
 24       1   0.0   11520  99.7    0.02
 21       2   0.0   11522  99.7    0.04
 17       2   0.0   11524  99.7    0.08
 -1      36   0.3   11560 100.0   36.08   (quality -1 = terminal quality 0)

Avg. full length: 11560.0, trimmed (qual > -1): 11524.0
Avg. quality: 84.9 per base

Initial, terminal qual 0 segments:  1-36, (None)

Regions of LLR- adjusted quality < 2.0:
1-38, 

2 regions, avg size 19.0, avg spacing 5780.0

First_start: 117, last_end: 11560
 Unused pair: cg050109r1 da040109r1  -8.3   0
LLR breakdown: discreps: -0.3 (<20 part: -0.3 (#=3), >20:0.0 (#=0); in HQ: -0.3, out HQ 0.0), match: 5.6  trail: -11.4  lead: -2.6  total: -8.7  223  1.18 0.00 0.00  cg050109r1      388   642 (389)    da040109r1       51   305 (791) *
 Unused pair: cc080109r1 cg050109r1  -6.3   4
LLR breakdown: discreps: -1.3 (<20 part: -1.3 (#=14), >20:0.0 (#=0); in HQ: 0.0, out HQ -1.3), match: 5.1  trail: 0.0  lead: -11.4  total: -7.6  157  0.00 0.00 5.58  cc080109r1      704   954 (135)  C cg050109r1   (389)   642   406 *
 Unused pair: ag020109r1 cg050109r1  -6.8   2
LLR breakdown: discreps: -0.2 (<20 part: -0.2 (#=13), >20:0.0 (#=0); in HQ: 0.0, out HQ -0.2), match: 3.2  lead: -10.8  total: -7.8  117  3.05 0.00 3.55  ag020109r1      818  1014 (0)  C cg050109r1   (389)   642   453  

Slack, # used pairs (max_score), unused
 0   277  (21.4)     1 (-8.3)     1079
 1   331  (21.2)     0 ( 0.0)      146
 2   202  (19.9)     1 (-6.8)        2
 3   124  (19.7)     0 ( 0.0)        0
 4    52  (19.2)     1 (-6.3)        0
 5    28  (18.1)     0 ( 0.0)        0
 6    45  (18.7)     0 ( 0.0)        0
 7    25  (19.7)     0 ( 0.0)        0
 8    20  (18.9)     0 ( 0.0)        0
 9    20  (18.9)     0 ( 0.0)        0
10    15  (18.9)     0 ( 0.0)        0
11    12  (16.5)     0 ( 0.0)        0
12     4  (16.8)     0 ( 0.0)        0
13     2  (10.3)     0 ( 0.0)        0
14     6  (17.4)     0 ( 0.0)        0
15     4  (15.0)     0 ( 0.0)        0
19     1  ( 0.0)     0 ( 0.0)        0
24     1  ( 0.0)     0 ( 0.0)        0
47     1  ( 0.0)     0 ( 0.0)        0
99     0  ( 0.0)    54 ( 6.6)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 1134 -  1556      423       ad060109f1   (  31)    No           1526
11561 - right        0+      ac060109r1   (11425)    No            135+

Bottom strand: 
 left -   535      535+      eh020109r1   (1478)    No           1478+
 2847 -  2980      134       cg050109f1   (3719)    Yes           873 
 5068 -  5108       41       dd120109r1   (5115)    Yes            48 
11561 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56  26554  26554 111056 (100.00)    16  0    0   0   0   0     0 (0.00)    0  2920 (2.63)
51   6336  32890  84502 ( 76.09)     3  0    0   0   0   0     0 (0.00)    0  2920 (3.46)
50   5015  37905  78166 ( 70.38)     0  0    0   0   0   0     0 (0.00)    0  2920 (3.74)
48    402  38307  73151 ( 65.87)     9  0    0   0   0   0     0 (0.00)    0  2920 (3.99)
47    905  39212  72749 ( 65.51)     5  0    0   0   0   0     0 (0.00)    0  2920 (4.01)
46   1352  40564  71844 ( 64.69)     9  0    0   0   0   0     0 (0.00)    0  2920 (4.06)
45   1196  41760  70492 ( 63.47)     3  0    0   0   0   0     0 (0.00)    0  2920 (4.14)
44   3970  45730  69296 ( 62.40)     6  0    0   0   0   0     0 (0.00)    0  2920 (4.21)
43   2408  48138  65326 ( 58.82)     2  0    0   0   0   0     0 (0.00)    0  2920 (4.47)
42   7116  55254  62918 ( 56.65)    16  0    0   0   0   0     0 (0.00)    0  2920 (4.64)
41    775  56029  55802 ( 50.25)     0  0    0   0   0   0     0 (0.00)    0  2920 (5.23)
40   4650  60679  55027 ( 49.55)    71  0    0   0   0   0     0 (0.00)    0  2920 (5.31)
39    267  60946  50377 ( 45.36)     2  0    0   0   0   0     0 (0.00)    0  2920 (5.80)
38    408  61354  50110 ( 45.12)     1  0    0   0   0   0     0 (0.00)    0  2920 (5.83)
37   2489  63843  49702 ( 44.75)    12  0    0   0   0   0     0 (0.00)    0  2920 (5.88)
36    256  64099  47213 ( 42.51)     5  0    0   0   0   0     0 (0.00)    0  2920 (6.18)
35   2335  66434  46957 ( 42.28)    26  0    0   0   0   0     0 (0.00)    0  2920 (6.22)
34    744  67178  44622 ( 40.18)    13  0    0   0   0   0     0 (0.00)    0  2920 (6.54)
33   1317  68495  43878 ( 39.51)    19  0    0   0   1   0     1 (0.08)    1  2920 (6.65)
32    992  69487  42561 ( 38.32)    51  0    0   0   0   0     0 (0.00)    1  2919 (6.86)
31    607  70094  41569 ( 37.43)    11  0    0   0   0   0     0 (0.00)    1  2919 (7.02)
30    754  70848  40962 ( 36.88)    17  0    0   0   0   0     0 (0.00)    1  2919 (7.13)
29   2262  73110  40208 ( 36.21)   103  0    0   0   6   0     6 (0.27)    7  2919 (7.26)
28    743  73853  37946 ( 34.17)    12  0    0   0   0   0     0 (0.00)    7  2913 (7.68)
27   1022  74875  37203 ( 33.50)    45  0    0   0   1   0     1 (0.10)    8  2913 (7.83)
26    436  75311  36181 ( 32.58)    41  0    0   0   1   0     1 (0.23)    9  2912 (8.05)
25   1195  76506  35745 ( 32.19)    69  0    0   0   1   1     2 (0.17)   11  2911 (8.14)
24   1054  77560  34550 ( 31.11)    64  0    0   0   2   1     3 (0.28)   14  2909 (8.42)
23    904  78464  33496 ( 30.16)    52  0    0   1   3   0     4 (0.44)   18  2906 (8.68)
22    784  79248  32592 ( 29.35)    55  0    0   0   2   0     2 (0.26)   20  2902 (8.90)
21   1067  80315  31808 ( 28.64)    57  0    0   2   3   0     5 (0.47)   25  2900 (9.12)
20    907  81222  30741 ( 27.68)    77  0    0   2   6   1     9 (0.99)   34  2895 (9.42)
19   1439  82661  29834 ( 26.86)   144  0    0   3  10   2    15 (1.04)   49  2886 (9.67)
18    920  83581  28395 ( 25.57)    81  0    0   2   7   0     9 (0.98)   58  2871 (10.11)
17   1025  84606  27475 ( 24.74)    93  0    0   8   6   0    14 (1.37)   72  2862 (10.42)
16   1135  85741  26450 ( 23.82)   137  0    0   5   5   2    12 (1.06)   84  2848 (10.77)
15   1494  87235  25315 ( 22.79)   126  0    0  22  15   0    37 (2.48)  121  2836 (11.20)
14   1159  88394  23821 ( 21.45)   129  0    0  14  15   1    30 (2.59)  151  2799 (11.75)
13   1865  90259  22662 ( 20.41)   212  0    0  41  15   3    59 (3.16)  210  2769 (12.22)
12   1702  91961  20797 ( 18.73)   165  0    0  49  31   4    84 (4.94)  294  2710 (13.03)
11   2595  94556  19095 ( 17.19)   209  0    0 119  40   6   165 (6.36)  459  2626 (13.75)
10   3127  97683  16500 ( 14.86)   341  0    0 174  82   9   265 (8.47)  724  2461 (14.92)
 9   5166 102849  13373 ( 12.04)   615  0    0 370 145  31   546 (10.57)  1270  2196 (16.42)
 8   3527 106376   8207 (  7.39)   431  0    0 358 200  18   576 (16.33)  1846  1650 (20.10)
 7   3028 109404   4680 (  4.21)   293  0    0 375 229  10   614 (20.28)  2460  1074 (22.95)
 6   1527 110931   1652 (  1.49)   311  0    0 209 195   5   409 (26.78)  2869  460 (27.85)
 4    116 111047    125 (  0.11)     6  0    0  32   8   1    41 (35.34)  2910   51 (40.80)
 0      9 111056      9 (  0.01)     0  0    6   0   3   1    10 (111.11)  2920   10 (111.11)
-1     32 111088      0 (  0.00)  21327  0    0   1   0   0     1 (3.12)  2921    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90  83052  83052 106639 (100.00)     0  0    0   0   0   0     0 (0.00)    0  2020 (1.89)
89    167  83219  23587 ( 22.12)     0  0    0   0   0   0     0 (0.00)    0  2020 (8.56)
88    161  83380  23420 ( 21.96)     0  0    0   0   0   0     0 (0.00)    0  2020 (8.63)
87     59  83439  23259 ( 21.81)     0  0    0   0   0   0     0 (0.00)    0  2020 (8.68)
86     74  83513  23200 ( 21.76)     0  0    0   0   0   0     0 (0.00)    0  2020 (8.71)
85    112  83625  23126 ( 21.69)     0  0    0   0   0   0     0 (0.00)    0  2020 (8.73)
84    107  83732  23014 ( 21.58)     0  0    0   0   0   0     0 (0.00)    0  2020 (8.78)
83     84  83816  22907 ( 21.48)     0  0    0   0   0   0     0 (0.00)    0  2020 (8.82)
82     99  83915  22823 ( 21.40)     0  0    0   0   0   0     0 (0.00)    0  2020 (8.85)
81    668  84583  22724 ( 21.31)     0  0    0   0   0   0     0 (0.00)    0  2020 (8.89)
80     42  84625  22056 ( 20.68)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.16)
79     87  84712  22014 ( 20.64)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.18)
78     45  84757  21927 ( 20.56)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.21)
77     76  84833  21882 ( 20.52)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.23)
76    141  84974  21806 ( 20.45)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.26)
75     85  85059  21665 ( 20.32)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.32)
74     36  85095  21580 ( 20.24)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.36)
73     73  85168  21544 ( 20.20)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.38)
72     57  85225  21471 ( 20.13)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.41)
71    116  85341  21414 ( 20.08)     1  0    0   0   0   0     0 (0.00)    0  2020 (9.43)
70     50  85391  21298 ( 19.97)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.48)
69    130  85521  21248 ( 19.93)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.51)
68     75  85596  21118 ( 19.80)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.57)
67    111  85707  21043 ( 19.73)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.60)
66   1738  87445  20932 ( 19.63)     0  0    0   0   0   0     0 (0.00)    0  2020 (9.65)
65    256  87701  19194 ( 18.00)     2  0    0   0   0   0     0 (0.00)    0  2020 (10.52)
64     38  87739  18938 ( 17.76)     0  0    0   0   0   0     0 (0.00)    0  2020 (10.67)
63     36  87775  18900 ( 17.72)     1  0    0   0   0   0     0 (0.00)    0  2020 (10.69)
62     78  87853  18864 ( 17.69)     2  0    0   0   0   0     0 (0.00)    0  2020 (10.71)
61    469  88322  18786 ( 17.62)     0  0    0   0   0   0     0 (0.00)    0  2020 (10.75)
60    164  88486  18317 ( 17.18)     0  0    0   0   0   0     0 (0.00)    0  2020 (11.03)
59     76  88562  18153 ( 17.02)     0  0    0   0   0   0     0 (0.00)    0  2020 (11.13)
58    107  88669  18077 ( 16.95)     0  0    0   0   0   0     0 (0.00)    0  2020 (11.17)
57    142  88811  17970 ( 16.85)     2  0    0   0   0   0     0 (0.00)    0  2020 (11.24)
56    552  89363  17828 ( 16.72)     0  0    0   0   0   0     0 (0.00)    0  2020 (11.33)
55     80  89443  17276 ( 16.20)     1  0    0   0   0   0     0 (0.00)    0  2020 (11.69)
54    270  89713  17196 ( 16.13)     0  0    0   0   0   0     0 (0.00)    0  2020 (11.75)
53    105  89818  16926 ( 15.87)     0  0    0   0   0   0     0 (0.00)    0  2020 (11.93)
52    297  90115  16821 ( 15.77)     1  0    0   0   0   0     0 (0.00)    0  2020 (12.01)
51    178  90293  16524 ( 15.50)     0  0    0   0   0   0     0 (0.00)    0  2020 (12.22)
50    212  90505  16346 ( 15.33)     2  0    0   0   0   0     0 (0.00)    0  2020 (12.36)
49    119  90624  16134 ( 15.13)     0  0    0   0   0   0     0 (0.00)    0  2020 (12.52)
48    122  90746  16015 ( 15.02)     1  0    0   0   0   0     0 (0.00)    0  2020 (12.61)
47    109  90855  15893 ( 14.90)     6  0    0   0   0   0     0 (0.00)    0  2020 (12.71)
46    151  91006  15784 ( 14.80)     3  0    0   0   0   0     0 (0.00)    0  2020 (12.80)
45    168  91174  15633 ( 14.66)     3  0    0   0   0   0     0 (0.00)    0  2020 (12.92)
44    235  91409  15465 ( 14.50)     1  0    0   0   0   0     0 (0.00)    0  2020 (13.06)
43    142  91551  15230 ( 14.28)     0  0    0   0   1   0     1 (0.70)    1  2020 (13.26)
42    184  91735  15088 ( 14.15)     7  0    0   0   0   0     0 (0.00)    1  2019 (13.38)
41    174  91909  14904 ( 13.98)     1  0    0   0   0   0     0 (0.00)    1  2019 (13.55)
40   3427  95336  14730 ( 13.81)    15  0    0   0   0   0     0 (0.00)    1  2019 (13.71)
39     56  95392  11303 ( 10.60)     2  0    0   0   2   0     2 (3.57)    3  2019 (17.86)
38     45  95437  11247 ( 10.55)     0  0    0   0   1   0     1 (2.22)    4  2017 (17.93)
37     46  95483  11202 ( 10.50)     5  0    0   0   0   0     0 (0.00)    4  2016 (18.00)
36     51  95534  11156 ( 10.46)     1  0    0   0   0   0     0 (0.00)    4  2016 (18.07)
35     75  95609  11105 ( 10.41)    15  0    0   0   0   0     0 (0.00)    4  2016 (18.15)
34    105  95714  11030 ( 10.34)     3  0    0   0   1   1     2 (1.90)    6  2016 (18.28)
33     74  95788  10925 ( 10.24)     6  0    0   3   1   0     4 (5.41)   10  2014 (18.43)
32     76  95864  10851 ( 10.18)    16  0    0   0   1   0     1 (1.32)   11  2010 (18.52)
31     40  95904  10775 ( 10.10)     4  0    0   0   2   0     2 (5.00)   13  2009 (18.65)
30     47  95951  10735 ( 10.07)     2  0    0   0   1   0     1 (2.13)   14  2007 (18.70)
29    100  96051  10688 ( 10.02)    46  0    0   0   6   0     6 (6.00)   20  2006 (18.77)
28     41  96092  10588 (  9.93)     6  0    0   0   1   0     1 (2.44)   21  2000 (18.89)
27     72  96164  10547 (  9.89)    11  0    0   0   2   0     2 (2.78)   23  1999 (18.95)
26     46  96210  10475 (  9.82)    27  0    0   0   2   0     2 (4.35)   25  1997 (19.06)
25    442  96652  10429 (  9.78)    18  0    0   0   3   1     4 (0.90)   29  1995 (19.13)
24    137  96789   9987 (  9.37)    27  0    0   0   3   0     3 (2.19)   32  1991 (19.94)
23    146  96935   9850 (  9.24)    20  0    0   0   5   0     5 (3.42)   37  1988 (20.18)
22     82  97017   9704 (  9.10)    22  0    0   2   4   0     6 (7.32)   43  1983 (20.43)
21    131  97148   9622 (  9.02)    11  0    0   2   4   0     6 (4.58)   49  1977 (20.55)
20    115  97263   9491 (  8.90)    29  0    0   1   6   1     8 (6.96)   57  1971 (20.77)
19    223  97486   9376 (  8.79)    48  0    0   3   9   1    13 (5.83)   70  1963 (20.94)
18     96  97582   9153 (  8.58)    20  0    0   2   7   0     9 (9.38)   79  1950 (21.30)
17    161  97743   9057 (  8.49)    14  0    0   6   4   0    10 (6.21)   89  1941 (21.43)
16    229  97972   8896 (  8.34)    34  0    0   2   4   1     7 (3.06)   96  1931 (21.71)
15    294  98266   8667 (  8.13)    27  0    0  20  14   0    34 (11.56)  130  1924 (22.20)
14    232  98498   8373 (  7.85)    31  0    0  12  12   1    25 (10.78)  155  1890 (22.57)
13    432  98930   8141 (  7.63)    38  0    0  26  15   3    44 (10.19)  199  1865 (22.91)
12    424  99354   7709 (  7.23)    26  0    0  30  23   4    57 (13.44)  256  1821 (23.62)
11    754 100108   7285 (  6.83)    28  0    0  80  23   6   109 (14.46)  365  1764 (24.21)
10   1045 101153   6531 (  6.12)    60  0    0 116  60   9   185 (17.70)  550  1655 (25.34)
 9   1843 102996   5486 (  5.14)   101  0    0 216  94  27   337 (18.29)  887  1470 (26.80)
 8   1411 104407   3643 (  3.42)    41  0    0 255 123  14   392 (27.78)  1279  1133 (31.10)
 7   1374 105781   2232 (  2.09)    51  0    0 260 163   9   432 (31.44)  1711  741 (33.20)
 6    760 106541    858 (  0.80)    33  0    0 134 131   4   269 (35.39)  1980  309 (36.01)
 4     91 106632     98 (  0.09)     0  0    0  25   6   1    32 (35.16)  2012   40 (40.82)
 0      7 106639      7 (  0.01)     0  0    4   0   3   1     8 (114.29)  2020    8 (114.29)
-1   4449 111088      0 (  0.00)  24620  0    2 592 295  12   901 (20.25)  2921    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      36       36        1
 17       2       38        1
 21       2       40        1
 24       1       41        1
 28       4       45        2
 29       1       46        2
 30       2       48        2
 33       1       49        2
 35       5       54        4
 37       2       56        4
 39       1       57        3
 40      13       70        6
 42       9       79       11
 43       8       87       14
 44       5       92       16
 45       1       93       16
 46       9      102       18
 47       5      107       21
 48       4      111       21
 49       2      113       21
 50      29      142       29
 51      84      226       40
 52      38      264       48
 53      18      282       52
 54      17      299       58
 55      19      318       61
 56     362      680       49
 57      12      692       51
 58       7      699       50
 59       3      702       52
 60      37      739       62
 61     190      929       80
 62      11      940       84
 63      10      950       85
 64       5      955       86
 65       8      963       87
 66     701     1664       39
 67      22     1686       43
 68      18     1704       47
 69      30     1734       53
 70      10     1744       53
 71      39     1783       55
 72      15     1798       57
 73      20     1818       57
 74      21     1839       58
 75      33     1872       57
 76      35     1907       62
 77      23     1930       65
 78      17     1947       60
 79      25     1972       52
 80      11     1983       47
 81     104     2087       46
 82      18     2105       48
 83      18     2123       49
 84      17     2140       52
 85      22     2162       47
 86      13     2175       52
 87      12     2187       50
 88      29     2216       52
 89      27     2243       58
 90    9317    11560        1

SS region: 1133 (9.80%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
 3687     -4.0  [-4.0,  0.0]  (1, 0)
 3708     -3.7  [-2.0,  0.0]  (0, 2)
 4334    -11.1  [-4.2,  0.0]  (0, 3)
 5467     -4.0  [-4.0,  0.0]  (0, 1)
 5814     -4.8  [-2.9,  0.0]  (0, 2)
 6572     -4.2  [-4.2,  0.0]  (0, 1)
 6712     -3.2  [-3.2,  0.0]  (0, 1)
 7720     -3.5  [-3.5,  0.0]  (0, 1)
 8630     -3.3  [-3.3,  0.0]  (0, 1)
 9322     -4.0  [-4.0,  0.0]  (0, 1)
 9968     -4.0  [-4.0,  0.0]  (0, 1)
10081     -3.7  [-3.7,  0.0]  (0, 1)
10791     -7.1  [-2.0,  0.0]  (0, 4)
11549     -4.0  [-2.3,  0.0]  (2, 0)
11558     -3.2  [-3.2,  0.0]  (1, 0)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)  1035- 1975 [19.0] (0,0)   C dd020109r1         1003-53 | 53 471  (527 1003) | DA:(**527 598**) || local(+/-) (9.2,0.0), distant (0.0,0.0)
(0, 0)  3091- 3686 [-0.3] (4,16)   C cg050109f1         629-34 || local(+/-) (13.3,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -0.1 (<20 part: -0.1 (#=1), >20:0.0 (#=0); in HQ: -0.1, out HQ 0.0), match: 13.3  trail: -13.5  lead: 0.0  total: -0.3 
Bypassed: (0, 0)  3091- 3686 [ 1.7] (16,16)     cg050109r1         47-642 || local(+/-) (12.5,13.3), distant (0.0,0.0)
Bypassed: (1, 0)  3432- 4289 [14.6] (0,0)     da040109r1         51-922 | 50 988 | DU:(952 988) [695 988  with   cb050109r1  792 1089-- displ. 536]  || local(+/-) (18.5,0.0), distant (0.9,0.0)
(0, 0)  3919- 4789 [16.9] (0,0)     cb050109r1         99-978 | 99 1090 | DU:(1023 1090) [793 1090  with   da040109r1  694 987-- displ. 536]  || local(+/-) (17.0,0.0), distant (6.2,0.0)
(585, 0)  5218- 5332 [-0.1] (0,0)   C ah020109r1         160-47 || local(+/-) (0.0,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -0.1 (<20 part: -0.1 (#=20), >20:0.0 (#=0); in HQ: 0.0, out HQ -0.1), match: 0.8  trail: 0.0  lead: -0.8  total: -0.1 
(0, 6)  5928- 6689 [13.5] (0,0)   C ch010109f1         800-37 | 20 833 | LU:(20 36)(801 833) || local(+/-) (15.7,0.0), distant (0.0,0.0)
(0, 0)  5991- 5998 [ 0.0] (0,59)     bb080109r1         14-21 | 50 80 | LU: || local(+/-) (0.0,0.0), distant (0.0,0.0)
(0, 885)  6876- 6883 [ 0.0] (0,0)     eg050109r1         895-902 | 10 52 | LU: || local(+/-) (0.0,0.0), distant (0.0,0.0)
(0, 914)  6982- 6991 [ 0.0] (0,0)     bd010109r1         933-942 | 15 49 | LU: || local(+/-) (0.0,0.0), distant (0.0,0.0)
(0, 1012)  7051- 7056 [ 0.0] (0,0)     ac030109r1         1021-1026 | 9 49 | LU: || local(+/-) (0.0,0.0), distant (0.0,0.0)
(22, 8)  6295- 7126 [11.2] (0,0)     cb020109r1         50-889 | 20 894 | LU:(**20 49**) || local(+/-) (18.3,0.0), distant (0.0,0.0)
(0, 0)  9137-10018 [16.2] (0,0)     cc060109r1         116-1003 | (40 118)  116 1026 | DU:(40 115) [40 118  with   ad090109r1  86 164]  CHIMERIC || local(+/-) (18.2,0.0), distant (0.0,0.0)
(16, 0) 10746-10803 [ 0.4] (0,0)   C ad010109r1         118-62 | (27 58)  62 118 | DU:(27 58) [27 58  with   ae120109r1  114 145]  CHIMERIC || local(+/-) (0.4,0.0), distant (0.0,0.0)
(0, 0) 11245-11560 [ 3.9] (0,0)     aa120109f1         56-377 | 56 776 | LU:(**378 776**) || local(+/-) (8.7,0.0), distant (0.0,0.0)
(0, 0) 11278-11560 [ 3.1] (54,0)     bf060109f1         29-318 | 29 724 | LU:(**319 724**) || local(+/-) (9.9,0.0), distant (0.0,0.0)

Gaps in unique-read coverage:   I 1005- 1556, I 4335- 5001

Contig 17.  386 reads; 29063 bp (untrimmed), 28954 (trimmed).
      1  1018 cd010109f1    890 (  0)  0.84 0.21 0.10    0 (103)   65 (110) 
     76  1068 dg120109f1    842 (  0)  1.78 1.04 0.00   28 ( 28)    8 ( 72) 
    362  1343 ec090109r1    872 (  0)  0.75 0.11 0.21   47 ( 47)    0 (  0) 
    598  1640 bh030109r1    690 (  0)  3.23 1.38 0.00   50 ( 50)  126 (233) 
    857  1883 bd100109r1    881 (  0)  0.92 1.02 0.00   48 ( 48)    0 (477) 
   1483  2426 eb120109r1    833 (  0)  0.56 0.11 0.00   49 (594)    0 (  0) 
   2055  3028 eg090109f1    873 (  0)  0.74 0.42 0.00   22 ( 22)    2 (  2) 
   2219  3177 ea020109f1    896 (  0)  0.21 0.21 0.00   21 ( 21)    0 (  0) 
   2304  3361 cd060109f1    895 (  0)  1.85 0.97 0.00   24 ( 24)    8 ( 40) 
   2396  3462 ae050109f1    796 (  0)  1.86 1.09 0.00   42 ( 42)  109 (141) 
C  2411  3400 dg120109r1    852 (  0)  1.38 0.32 0.21    0 (  0)   49 ( 49) 
   2584  3620 ca070109r1    835 (  0)  1.18 1.18 0.00   50 ( 50)   52 ( 96) 
   2600  3577 cc120109r1    865 (  0)  1.07 0.32 0.00   47 ( 47)    0 (  0) 
C  2714  3722 bd100109f1    855 (  0)  1.64 1.03 0.10   13 ( 96)   23 ( 23) 
C  2942  3944 cd010109r1    867 (  0)  1.37 0.11 0.11    6 (  6)   49 ( 49) 
C  2968  4006 dd100109r1    225 (  0)  1.19 0.00 0.00  742 (726)   45 ( 45) 
   3274  4268 ee050109f1    892 (  0)  0.83 0.41 0.00   24 ( 24)    5 (  3) 
   3279  4306 ca080109r1    793 (  0)  1.07 2.03 0.11   49 ( 49)   43 ( 88) 
   3323  4303 cb120109r1    845 (  0)  1.19 0.43 0.00   52 ( 43)    8 ( 35) 
   3325  4340 cc100109r1    856 (  0)  1.36 0.84 0.00   50 ( 41)   11 ( 15) 
   3469  4525 ce020109r1    813 (  0)  0.33 1.22 0.11   46 ( 46)  107 ( 94) 
C  3520  4491 eg090109r1    848 (  0)  1.30 0.11 0.00    0 ( 22)   51 ( 51) 
   3537  4576 ch030109f1    811 (  0)  0.67 0.67 0.33   25 ( 25)  115 (115) 
C  3579  4604 ch030109r1    748 (  0)  1.73 2.60 0.22   56 (198)   47 ( 47) 
   3681  4728 dd100109f1    224 ( 31)  0.00 0.40 0.40   29 ( 13)  768 (768) 
C  3687  4699 cc100109f1    876 (  0)  1.97 0.21 0.10   24 ( 43)   23 (  9) 
C  3729  4702 cb120109f1    874 (  0)  0.64 0.64 0.21    4 (  0)   26 ( 12) 
C  3774  4713 eb120109f1    865 (  0)  0.22 0.66 0.11    3 (  3)   21 ( 21) 
C  3846  4921 cd060109r1    852 (  0)  1.12 2.04 0.10   46 (129)   49 ( 49) 
    -44  1066 da070109r1      7 (  0)  0.00 0.00 0.00  359 (105)  744 (536) 
   3884  4912 ab020109f1    740 (  0)  4.43 1.69 0.11   28 ( 32)   53 (235) 
C  3975  4934 ea020109r1    854 (  0)  0.77 0.55 0.00    8 ( 42)   46 ( 46) 
   4191  5228 cb070109r1    842 (  0)  0.64 1.50 0.11   47 ( 47)   56 (129) 
   4302  5220 eh010109r1    832 (  0)  0.46 0.23 0.12   46 ( 46)    5 (  5) 
   4601  5688 ca100109f1    849 (  0)  0.65 0.86 0.22   99 ( 99)   59 ( 91) 
   4647  5618 eh060109f1    883 (  0)  0.53 0.53 0.11   26 ( 26)    4 ( 23) 
C  4653  5683 bh030109f1    640 (  0)  2.96 0.40 0.13  255 (285)   34 ( 39) 
C  4712  5705 ee050109r1    877 (  0)  0.64 0.11 0.32   10 ( 23)   49 ( 49) 
   4739  5889 ag090109f1    850 (  0)  1.56 0.63 0.31  167 (167)   25 ( 85) 
   4763  5791 cg030109r1    846 (  0)  0.65 0.97 0.00   48 ( 48)   56 ( 86) 
C  4826  5808 cc120109f1    895 (  0)  0.31 0.63 0.10    2 (  6)   25 ( 25) 
   4901  6037 cd110109r1    744 ( 31)  1.44 0.96 0.00  147 (147)  157 (177) 
   4924  5955 af040109f1    884 (  0)  1.24 0.41 0.10   28 ( 28)   38 ( 82) 
C  4982  6011 ce020109f1    889 (  0)  1.60 1.00 0.10    4 ( 83)   23 ( 23) 
   5012  6037 bc110109r1    720 (  0)  1.82 1.09 0.00   52 ( 52)  150 (168) 
C  5038  6106 ae050109r1    818 (  0)  1.53 0.98 0.00  106 (174)   46 ( 46) 
   5078  6107 dc100109f1    163 (  0)  22.50 0.67 0.34   26 ( 30)  115 (371) 
   5169  6295 ad080109f1    876 (  0)  0.42 0.85 0.00   74 ( 78)  109 (108) 
C  5279  6346 cd110109f1    807 (  0)  1.91 1.06 0.32   55 (119)   73 ( 73) 
   5365  6311 eg120109f1    212 ( 46)  20.07 2.24 0.94   38 ( 38)   62 (140) 
C  5370  6409 cb070109f1    881 (  0)  1.72 0.81 0.00   19 ( 61)   33 ( 33) 
C  5377  6444 ca070109f1    853 (  0)  0.88 0.33 0.00  114 (114)   42 ( 24) 
   5396  6455 dd050109f1    340 (  0)  2.13 2.36 0.00  591 (591)   46 ( 76) 
C  5401  6427 da070109f1    827 (  0)  2.82 0.81 0.50   11 ( 59)   23 (  7) 
   5443  6494 ba050109f1    723 (  0)  1.92 1.08 0.00  107 (106)  112 (151) 
   5465  6529 bg080109f1    744 (  0)  2.01 0.71 0.00   27 ( 27)  194 (196) 
   5538  6599 bh050109r1    756 (  0)  0.60 1.20 0.00   49 ( 49)  180 (180) 
   5549  6540 bf010109f1    688 (334)  2.29 2.75 0.11   32 ( 32)   86 (164) 
   5606  6547 ec120109r1    816 (312)  1.34 0.56 0.00   49 ( 49)    0 ( 32) 
C  5612  6659 dg080109f1    852 (228)  0.66 0.55 0.00  109 (123)   28 ( 28) 
   5631  6672 ce090109f1    913 (317)  1.58 0.59 0.10   23 ( 13)    6 ( 43) 
   5634  6690 de080109f1    830 (304)  0.76 1.09 0.11   20 ( 11)  120 (120) 
   5639  6613 ea040109r1    870 (280)  0.76 0.22 0.11   49 ( 49)    0 ( 27) 
C  5670  6710 ab020109r1    607 ( 88)  7.56 1.33 0.44   82 (241)   59 ( 94) 
C  5679  6705 ca080109f1    878 (225)  1.22 0.92 0.10    7 ( 54)   38 ( 38) 
   5674  6733 dg080109r1    779 (260)  1.37 1.02 0.11   46 ( 46)  135 (169) 
   5683  6700 bg010109f1    627 (207)  3.61 1.81 0.84   33 ( 33)  154 (253) 
C  5808  6852 bg080109r1    788 ( 36)  1.56 0.78 0.45   97 (121)   51 ( 51) 
   5817  6859 bb040109r1    814 (117)  1.87 1.77 0.10   45 ( 45)   36 (132) 
   5896  6879 db120109r1    398 (  0)  13.43 1.64 0.33   61 ( 61)    7 ( 59) 
C  5904  6944 ba050109r1    763 (  0)  2.65 1.21 0.11   85 (204)   50 ( 50) 
   5915  6923 be010109r1    867 (  0)  1.04 1.04 0.00   51 ( 53)    0 ( 47) 
C  6154  7079 eh010109f1    845 (  0)  0.78 0.11 0.22    0 (  4)   26 ( 26) 
C  6189  7221 cg030109f1    879 (  0)  0.84 0.63 0.00   57 ( 57)   29 ( 29) 
   6249  7285 dd010109f1    668 (  0)  1.13 0.14 0.00   43 ( 43)  285 (285) 
   6298  7259 eb110109r1    853 (  0)  0.77 0.22 0.11   56 ( 56)    0 ( 11) 
C  6513  7444 eg120109r1    165 (  0)  21.31 2.93 0.82   24 (242)   54 (135) 
C  6540  7528 db120109f1    753 (  0)  1.87 1.17 0.00   38 ( 38)   94 (104) 
C  6542  7588 af040109r1    532 (  0)  1.85 0.50 0.00  403 (422)   48 ( 48) 
C  6966  7993 bc110109f1    728 (  0)  1.20 1.44 0.24  162 (189)   31 ( 31) 
   6966  8005 ce060109r1    869 (  0)  1.83 0.71 0.10   53 ( 53)    5 ( 63) 
C  7045  8101 dd050109r1    833 (  0)  0.85 1.60 0.00   74 (117)   46 ( 46) 
C  7136  8198 ad080109r1    860 (  0)  0.94 1.36 0.10   57 ( 81)   47 ( 47) 
C  7212  8247 bh050109f1    774 (  0)  0.48 1.20 0.12  172 (172)   28 ( 28) 
C  7209  8178 eh060109r1    866 (  0)  1.09 0.33 0.00    3 (  3)   46 ( 46) 
   7292  8275 bd110109f1    904 (  0)  1.05 0.21 0.00   32 ( 32)    2 (  0) 
   7311  8316 ch090109f1    915 (  0)  1.63 0.20 0.00   26 ( 26)    1 (  1) 
   7362  8393 bc030109r1    889 (  0)  1.93 0.81 0.00   42 ( 41)    4 ( 54) 
C  7391  8411 dc100109r1    819 (  0)  0.96 2.14 0.00   33 (112)   53 ( 53) 
C  7392  8466 ce090109r1    806 (  0)  0.87 2.17 0.00  106 (145)   49 ( 49) 
C  7404  8497 ca100109r1    799 (  0)  1.78 1.22 0.00   74 (106)  120 (120) 
C  7411  8466 de080109r1    813 (  0)  1.91 1.80 0.00   62 (161)   52 ( 52) 
C  7507  8520 bf010109r1    765 (  0)  1.72 1.49 0.00   91 (117)   49 ( 49) 
C  7562  8685 ag090109r1    841 (  0)  2.29 1.04 0.00   14 ( 18)  150 (150) 
C  7567  8568 be010109f1    831 (  0)  0.97 1.51 0.00   43 ( 48)   32 ( 32) 
C  7706  8736 bc030109f1    890 (  0)  0.83 0.94 0.00   41 ( 40)   29 ( 29) 
C  7707  8686 ea040109f1    893 (  0)  0.74 0.43 0.00   12 ( 41)   28 ( 28) 
   7891  8870 eb060109r1    860 (  0)  1.52 0.33 0.00   48 ( 48)   10 ( 23) 
   8216  9183 ea070109r1    842 (  0)  1.54 0.44 0.00   52 ( 52)    4 ( 54) 
C  8301  9391 aa100109f1    747 (  0)  2.96 1.03 0.11  117 (171)   96 ( 96) 
   8334  9430 cd070109r1    694 (  0)  5.18 0.81 0.00   52 ( 55)  177 (255) 
   8339  9390 ad070109r1    820 (  0)  1.82 0.96 0.32   44 ( 49)   75 ( 97) 
   8377  9347 eb090109r1    879 (  0)  0.54 0.54 0.00   44 ( 44)    3 ( 18) 
   8530  9504 ef090109r1    844 (  0)  1.30 0.86 0.11   49 ( 49)    0 ( 50) 
   8532  9509 eb070109r1    866 (  0)  1.50 0.21 0.11   47 ( 47)    0 ( 12) 
   8547  9530 ef070109f1    861 (  0)  1.79 0.63 0.00   30 ( 30)    6 ( 35) 
C  8601  9588 ef070109r1    773 (  0)  1.68 1.79 0.00   44 (103)   49 ( 49) 
   8789  9767 ec080109r1    875 (  0)  0.86 0.32 0.21   44 ( 44)    0 ( 29) 
C  8808  9783 ea030109f1    856 (  0)  0.56 0.33 0.00   50 ( 54)   28 ( 25) 
   8815  9777 ea030109r1    848 (  0)  0.89 0.00 0.11   47 ( 47)   22 ( 19) 
   8889  9909 bf030109r1    882 (  0)  1.64 0.51 0.10   44 ( 44)    3 ( 61) 
C  8944 10003 ce060109f1    834 (  0)  0.85 1.60 0.00   97 (175)   24 ( 24) 
   8980 10013 bf070109r1    850 (  0)  1.39 0.64 0.00   50 ( 50)   52 ( 82) 
C  9040 10048 bd110109r1    861 (  0)  1.35 1.04 0.00    0 (  2)   49 ( 49) 
C  9042 10047 ch090109r1    880 (  0)  0.94 0.73 0.00    0 (  0)   48 ( 48) 
C  9103 10153 bb040109f1    797 (  0)  1.09 1.86 0.11  109 (165)   28 ( 28) 
C  9107 10057 ec120109f1    863 (  0)  0.76 0.22 0.11    8 (  8)   26 ( 26) 
   9246 10249 df110109r1    862 (  0)  0.74 1.05 0.11   49 ( 49)    6 (  6) 
   9327 10329 cf110109r1    860 (  0)  1.59 0.32 0.21   51 ( 51)    9 ( 52) 
C  9332 10318 eb060109f1    894 (  0)  1.46 0.10 0.00    0 (  5)   26 ( 26) 
C  9433 10396 eb110109f1    871 (  0)  0.54 0.43 0.32    0 (  0)   30 ( 30) 
   9567 10603 bh060109r1    747 (  0)  1.37 0.37 0.00   50 ( 50)  182 (218) 
C  9595 10559 ea070109f1    881 (  0)  0.75 0.53 0.00    4 (  9)   22 ( 22) 
C  9720 10724 cf110109f1    904 (  0)  1.13 0.51 0.00    0 (  0)   29 ( 29) 
  10030 11079 cb080109r1    798 (  0)  2.87 1.44 0.51   56 ( 56)   20 ( 64) 
  10053 11105 cf030109r1    809 (  0)  1.13 0.68 0.23   48 ( 48)  123 (128) 
C 10075 11067 eb070109f1    875 (  0)  0.53 1.06 0.00   24 ( 30)   27 ( 12) 
C 10086 11064 ef090109f1    881 (  0)  0.42 1.26 0.00    2 ( 21)   24 (  8) 
C 10141 11272 cd070109f1    792 (  0)  3.23 1.46 0.10   79 (183)   93 ( 91) 
C 10151 11204 ad070109f1    880 (  0)  0.73 1.14 0.10   66 ( 79)   25 ( 23) 
C 10172 11150 eb090109f1    922 (  0)  0.63 0.00 0.00    0 (  0)   26 ( 24) 
C 10221 11241 bf070109f1    861 (  0)  1.18 0.64 0.00   69 ( 63)   21 ( 21) 
  10248 11267 cg040109r1    851 (  0)  2.80 0.52 0.00   46 ( 46)    9 ( 70) 
  10305 11316 ah110109r1    772 (  0)  0.93 1.62 0.00   46 ( 46)  103 (178) 
C 10348 11354 bf030109f1    883 (  0)  2.15 0.41 0.00    5 ( 92)   27 ( 27) 
  10347 11353 cb010109r1    835 (  0)  1.19 1.08 0.11   48 ( 48)   33 ( 68) 
  10656 11665 ac020109r1    793 (  0)  2.70 1.97 0.10   46 ( 51)    1 (127) 
  10653 11704 cd050109r1    889 (  0)  1.33 1.02 0.00   52 ( 52)   20 ( 20) 
C 10752 11756 df110109f1    874 (  0)  1.84 0.82 0.00    5 ( 75)   23 ( 23) 
  10796 11818 ab100109r1    823 (  0)  1.74 0.98 0.00   47 ( 47)   57 ( 96) 
  10802 11755 ef110109r1    850 (  0)  0.68 0.23 0.00   47 ( 47)   19 ( 29) 
  10837 11819 ag010109r1    832 (  0)  2.25 0.75 0.00   50 ( 50)    0 ( 57) 
  10988 12025 df040109r1    882 (  0)  1.07 0.43 0.00   44 ( 44)   56 ( 92) 
  11054 12062 ba010109r1    827 (  0)  1.59 1.17 0.42   51 ( 51)   15 (127) 
  11114 12126 dh070109r1    877 (  0)  1.26 0.63 0.21   48 ( 48)   10 ( 10) 
C 11355 12392 cf030109f1    845 (  0)  1.98 1.14 0.00   50 (140)   26 ( 26) 
  11398 12369 eb020109r1    872 (  0)  0.54 0.54 0.11   47 ( 47)    0 (  0) 
  11442 12443 bh020109r1    720 (  0)  3.58 0.58 0.46   44 ( 44)   93 (125) 
  11495 12524 ca050109f1    855 (  0)  1.73 1.02 0.41   27 ( 27)   19 ( 88) 
C 11501 12488 ec080109f1    912 (  0)  0.62 0.10 0.21    4 (  4)   22 ( 22) 
C 11571 12576 ab100109f1    831 (  0)  1.65 1.75 0.00   12 (120)   24 ( 24) 
  11629 12659 af030109f1    848 (  0)  0.43 1.19 0.11   24 ( 24)   79 ( 79) 
C 11873 12914 cb080109f1    850 (  0)  1.13 1.64 0.21   44 (115)   23 ( 23) 
C 11969 13022 ac020109f1    704 (  0)  2.70 0.86 0.00  209 (209)   29 ( 29) 
C 12014 13014 bh060109f1    760 (  0)  2.82 0.76 0.54   59 (141)   21 ( 25) 
C 12087 13066 eh040109f1    466 (  0)  0.21 0.21 0.00  480 (480)   22 (  8) 
C 12190 13220 cb010109f1    854 (  0)  1.97 0.73 0.10   20 ( 62)   46 ( 45) 
C 12268 13308 cd050109f1    903 (  0)  1.28 0.99 0.20    8 (  8)   21 ( 21) 
  12260 13289 dh060109f1    797 (  0)  2.36 1.07 0.21   29 ( 29)   69 (150) 
  12282 13253 eh070109r1    830 (  0)  0.78 0.89 0.00   46 ( 46)   28 ( 83) 
  12307 13324 af100109f1    902 (  0)  0.71 1.12 0.00   28 ( 28)    7 ( 27) 
C 12314 13268 ef110109f1    898 (  0)  0.43 0.00 0.00    2 (  2)   24 ( 24) 
C 12334 13339 bh020109f1    739 (  0)  2.30 1.72 0.00  107 (133)   29 ( 29) 
C 12349 13334 ah110109f1    861 (  0)  1.26 1.05 0.00   11 ( 32)   23 ( 30) 
  12431 13413 bf110109f1    833 (  0)  2.19 1.25 0.00   23 ( 23)    0 (136) 
  12437 13424 ac120109r1    791 (  0)  2.47 1.51 0.00   55 ( 90)    3 ( 90) 
C 12467 13508 cg040109f1    865 (  0)  1.03 1.44 0.10   30 ( 58)   38 ( 38) 
C 12512 13509 ba010109f1    852 (  0)  1.25 1.46 0.00   10 ( 10)   27 ( 27) 
  12520 13489 eh040109r1    453 (  0)  0.63 0.63 0.00   47 ( 47)  445 (429) 
C 12593 13721 cb050109f1    821 (  0)  2.25 0.43 0.21  119 (119)   78 ( 78) 
C 12656 13793 dh070109f1    791 (  0)  0.57 1.14 0.11  143 (164)  119 (119) 
  12757 13889 ah100109r1    730 (  0)  1.15 2.08 0.00  144 (144)  123 (199) 
C 12802 13851 ca050109r1    781 (  0)  1.00 1.45 0.11  100 (145)   52 ( 52) 
  12833 13906 cc040109f1    732 (  0)  3.01 0.46 0.00   38 ( 43)  172 (198) 
  12917 14045 ad110109r1    801 (  0)  1.72 1.18 0.00  171 (171)   29 ( 29) 
  13039 14055 dc010109f1    847 (  0)  1.36 0.31 0.42   30 ( 30)   31 ( 31) 
C 13057 14096 df040109f1    856 (  0)  1.89 1.29 0.00    6 ( 69)   28 ( 28) 
  13248 14385 dh090109f1    418 (  0)  10.19 1.32 0.26  125 (125)  257 (248) 
C 13250 14228 ag010109f1    818 (  0)  1.41 0.33 0.11   32 ( 83)   25 ( 27) 
C 13315 14342 af030109r1    801 (  0)  1.27 1.48 0.11   37 ( 77)   48 ( 48) 
  13353 14360 eb030109f1    486 (  0)  11.26 2.01 0.22   32 ( 87)   79 (212) 
  13443 14413 bb120109f1    872 (  0)  0.22 0.22 0.00   36 ( 36)    6 (  6) 
  13463 14491 bc070109r1    850 (  0)  0.82 1.44 0.00   48 ( 48)    6 (  6) 
  13463 14467 cg110109r1    796 (  0)  2.23 1.06 0.00   49 ( 49)   16 (113) 
  13528 14515 ba110109f1    805 (  0)  1.48 0.95 0.32   36 ( 36)    3 ( 43) 
  13530 14566 cc020109f1    830 (  0)  1.95 0.72 0.20   42 ( 42)   19 ( 94) 
  13544 14661 ac100109r1    201 (  0)  15.74 0.46 0.15  217 (221)  253 (496) 
C 13706 14725 af100109r1    829 (  0)  1.14 1.25 0.10   13 ( 32)   46 ( 46) 
C 13761 14738 eb020109f1    872 (  0)  0.74 0.32 0.00    1 (  1)   26 ( 26) 
  13763 14747 ec050109f1    869 (  0)  0.52 0.31 0.21   22 ( 22)    9 (  1) 
  13768 14821 ca030109f1    847 (  0)  1.26 0.63 0.00   24 ( 24)   75 ( 76) 
C 13824 14825 bf110109r1    858 (  0)  0.74 0.42 0.21    2 (  3)   49 ( 49) 
  13921 14910 ec060109f1    899 (  0)  0.62 0.10 0.00   25 ( 25)    0 (  0) 
  13933 14931 bh010109f1    457 (  0)  4.67 0.83 0.00  119 (124)  280 (373) 
C 13979 15009 dh060109r1    763 (  0)  1.17 2.86 0.00   35 ( 80)   53 ( 53) 
C 13979 15026 ac120109f1    793 (  0)  1.50 1.39 0.21   20 ( 68)   92 ( 92) 
C 14083 15091 bc070109f1    859 (  0)  1.75 0.51 0.00   12 ( 12)   26 ( 28) 
C 14092 15089 cg110109f1    843 (  0)  1.45 1.03 0.00    5 ( 89)   26 ( 26) 
C 14127 15134 ah100109f1    796 (  0)  2.67 0.72 0.41   11 ( 52)   24 ( 24) 
  14187 15203 ag030109r1    772 (  0)  3.63 0.41 0.41   47 ( 47)    6 ( 70) 
  14293 15238 ef010109f1    823 (  0)  0.77 0.44 0.22   29 ( 29)    2 (  2) 
C 14380 15402 ad110109f1    758 (  0)  0.23 1.62 0.00  136 (136)   23 ( 23) 
C 14468 15433 eh070109f1    862 (  0)  0.75 0.21 0.00    3 ( 24)   25 ( 25) 
C 14513 15537 dc010109r1    707 (  0)  2.06 1.83 0.00  101 (130)   50 ( 95) 
C 14686 15714 ca030109r1    819 (  0)  2.27 0.41 0.21   17 (106)   43 ( 43) 
C 14726 15738 cc020109r1    815 (  0)  1.48 0.74 0.00   16 ( 69)   50 ( 50) 
C 14730 15720 bb100109f1    771 (  0)  1.24 0.45 0.11   81 ( 85)   24 ( 24) 
  14751 15784 bb100109r1    782 (  0)  1.56 0.22 0.22   47 ( 47)   88 ( 87) 
  15038 16068 bc080109f1    876 (  0)  1.42 0.51 0.00   25 ( 25)   17 ( 39) 
  15120 16170 dd030109r1    784 (  0)  2.51 0.77 0.00   50 ( 53)   86 (141) 
  15123 16183 ba060109f1    745 (  0)  1.61 0.81 0.23   32 ( 32)  161 (161) 
C 15351 16520 ac100109f1    425 (  0)  7.40 0.47 0.16  377 (416)  158 (158) 
C 15439 16418 ba110109r1    794 (  0)  2.39 0.65 0.00   13 ( 34)   47 ( 47) 
  15449 16476 ba030109f1    823 (  0)  0.93 1.96 0.10   23 ( 23)   37 (103) 
C 15615 16582 bb120109r1    852 (  0)  0.66 0.22 0.00   10 ( 10)   48 ( 48) 
C 15754 16739 ec060109r1    864 (  0)  0.85 0.11 0.21    0 (  5)   47 ( 47) 
C 15836 16788 eb030109r1    486 (  0)  8.44 2.36 0.12   90 (300)   57 ( 86) 
  15921 16883 ea010109f1    857 (  0)  0.21 0.85 0.00   26 ( 15)    1 (  0) 
  15924 16956 ad090109f1    795 (  0)  0.86 1.72 0.11   25 ( 13)   80 ( 71) 
  16173 17197 ag100109f1    838 (  0)  1.21 1.01 0.10   25 ( 25)    5 ( 26) 
C 16205 17262 dd030109f1    753 (  0)  2.01 1.27 0.21   80 (126)   35 ( 35) 
C 16227 17231 bh010109r1    592 (  0)  3.24 1.30 0.00  186 (197)   47 ( 47) 
C 16430 17489 ba060109r1    690 (  0)  1.02 2.49 0.00  125 (175)   50 ( 50) 
C 16426 17503 cc040109r1    679 (  0)  1.75 1.51 0.00  169 (170)   50 ( 50) 
  16435 17478 dc080109f1    813 (  0)  1.22 1.02 0.00   27 ( 27)   32 ( 74) 
C 16548 17585 ba030109r1    812 (  0)  1.12 1.53 0.00    7 (  3)   48 ( 48) 
C 16543 17524 ec050109r1    816 (  0)  0.53 0.64 0.00    0 (  0)   46 ( 46) 
  16742 17701 ef020109f1    859 (  0)  0.43 0.11 0.11   24 ( 24)    0 (  0) 
C 16866 17907 ag030109f1    775 (  0)  1.74 1.41 0.11   85 (154)   38 ( 38) 
  16877 17844 ea090109f1    870 (  0)  0.21 0.43 0.00   26 ( 26)    8 (  8) 
  17003 17994 dc120109f1    820 (  0)  0.86 1.50 0.00   26 ( 26)   32 ( 52) 
C 17289 18297 bd030109f1    471 (  0)  0.41 0.20 0.00  498 (498)   21 ( 13) 
  17404 18402 ed040109f1    919 (  0)  0.31 0.41 0.10   27 ( 27)    8 ( 13) 
  17433 18447 bd090109f1    874 (  0)  1.24 1.13 0.00   25 ( 25)   20 ( 75) 
C 17463 18495 bc080109r1    867 (  0)  1.34 0.72 0.41   19 ( 61)   44 ( 43) 
C 17511 18644 ad090109r1    814 ( 76)  2.31 1.15 0.21   18 ( 90)  163 (163) 
  17553 18560 ae120109f1    838 (111)  1.08 1.08 0.00   26 ( 15)   55 ( 55) 
  17555 18508 ea110109f1    871 (118)  1.08 0.32 0.00   24 ( 14)    0 (  0) 
  17558 18543 ed070109f1    911 (130)  0.63 0.31 0.00   25 ( 25)    3 ( 28) 
  17578 18585 bh100109f1    807 ( 48)  3.70 1.03 0.00   33 ( 37)    1 (132) 
  17738 18771 bd030109r1    478 (  0)  0.00 0.20 0.00   48 ( 48)  495 (486) 
  17880 18924 cc070109f1    866 (  0)  0.43 1.07 0.11   40 ( 40)   67 ( 67) 
C 17894 18847 ea010109r1    873 (  0)  0.77 0.00 0.00    0 ( 22)   48 ( 48) 
  17939 18876 eg010109f1    831 (  0)  1.55 0.44 0.00   25 ( 25)   10 ( 18) 
  17947 18960 ce010109f1    876 (  0)  1.46 0.62 0.10   28 ( 28)   25 ( 75) 
  18085 19094 ba090109f1    818 (  0)  1.93 1.07 0.11   25 ( 25)   53 (138) 
  18226 19369 dh100109f1    673 (  0)  2.80 1.02 0.00  121 (121)  237 (237) 
  18245 19288 df070109f1    876 (  0)  1.69 1.49 0.00   31 ( 29)    7 ( 39) 
C 18248 19159 ef010109r1    838 (  0)  1.13 0.11 0.00    1 (  6)   25 ( 25) 
  18255 19276 cd020109f1    835 (  0)  1.73 1.93 0.10   21 ( 19)   18 (143) 
  18430 19416 ee030109f1    915 (  0)  0.52 0.10 0.00   26 ( 26)    4 (  4) 
  18487 19488 ch020109f1    851 (  0)  1.84 0.61 0.51   23 ( 23)    0 ( 59) 
C 18507 19507 dc120109r1    821 (  0)  0.88 1.21 0.00   19 ( 47)   74 ( 74) 
C 18609 19692 dh100109r1    584 (  0)  4.64 0.55 0.00  252 (267)   99 (140) 
C 18785 19839 dc080109r1    830 (  0)  1.06 1.80 0.00   59 ( 81)   51 ( 51) 
  18821 19788 bc120109f1    863 (  0)  1.06 0.42 0.32   24 ( 24)    2 (  2) 
C 18863 19837 ed070109r1    868 (  0)  1.08 0.32 0.00    0 (  0)   47 ( 47) 
  18867 19924 de020109f1    855 (  0)  1.08 0.65 0.00   30 ( 30)  103 (124) 
C 18882 19835 ea090109r1    836 (  0)  1.54 0.33 0.00    0 ( 47)   47 ( 47) 
  18931 19984 dh030109f1    808 (  0)  1.30 1.52 0.11   41 ( 32)   91 (139) 
  18947 19956 aa010109f1    836 (  0)  1.17 1.39 0.00   26 ( 17)   47 ( 85) 
  19018 20038 ae040109f1    851 (  0)  1.23 1.64 0.10   24 ( 24)   20 (100) 
  19159 20185 dc020109f1    885 (  0)  1.62 0.81 0.00   28 ( 28)   11 ( 78) 
  19177 20204 cf020109f1    876 (  0)  0.82 1.13 0.21   28 ( 28)   26 ( 52) 
C 19178 20204 ba090109r1    803 (  0)  0.59 0.47 0.00  125 (125)   49 ( 49) 
C 19197 20187 ec070109f1    281 (  0)  0.96 0.96 0.00  654 (654)   25 ( 16) 
  19292 20293 cg010109f1    865 (  0)  1.15 1.05 0.00   33 ( 33)   13 ( 13) 
C 19388 20422 bh100109r1    761 (  0)  1.79 1.90 0.00   85 (201)   54 ( 54) 
  19522 20533 ca010109f1    842 (  0)  2.09 0.63 0.21   24 ( 24)   30 ( 34) 
C 19554 20563 ce010109r1    822 (  0)  1.40 1.19 0.00   37 ( 80)   47 ( 47) 
C 19555 20651 ae120109r1    814 (  0)  2.26 0.86 0.00   20 ( 20)  146 (146) 
C 19582 20603 df070109r1    815 (  0)  2.97 1.13 0.10    3 ( 93)   43 ( 43) 
  19716 20724 ac110109f1    887 (  0)  1.63 0.20 0.20   26 ( 26)    3 ( 28) 
C 19773 21351 bg070109r1      6 (  0)  0.00 0.00 0.00  109 (1475) 1462 ( 73) 
  19801 20772 ec070109r1    286 (  0)  1.28 0.32 0.00   50 ( 50)  610 (601) 
C 19820 20772 ef020109r1    875 (  0)  0.11 0.11 0.00    0 (  0)   48 ( 48) 
  20091 21182 dh050109f1    777 (  0)  1.04 1.15 0.12   32 ( 36)  194 (205) 
C 20104 21142 cc070109r1    829 (  0)  0.90 0.56 0.00   99 (131)   50 ( 50) 
C 20110 21129 bd090109r1    826 (  0)  2.09 1.26 0.10   16 ( 61)   48 ( 48) 
C 20153 21126 ee030109r1    883 (  0)  0.54 0.32 0.00    0 (  0)   47 ( 47) 
C 20208 21186 bc120109r1    833 (  0)  0.97 1.40 0.00    3 ( 77)   50 ( 50) 
  20208 21244 bg070109f1    607 (  0)  5.79 0.51 0.13   36 ( 36)  224 (324) 
  20234 21324 dc050109f1    859 (  0)  0.84 1.57 0.00   41 ( 41)   93 (125) 
C 20251 21311 de070109r1    512 (  0)  0.19 0.00 0.00  496 (491)   48 ( 48) 
C 20268 21342 ab090109r1      6 (  0)  11.11 0.00 0.00 1010 (1006)   56 ( 27) 
C 20283 21268 ed040109r1    867 (  0)  1.49 0.32 0.11    0 ( 28)   48 ( 48) 
C 20264 21335 ch070109r1      5 (  0)  0.00 0.00 0.00   23 (981) 1043 ( 51) 
C 20471 21470 ch020109r1    851 (  0)  1.61 0.86 0.00   20 ( 62)   47 ( 47) 
  20505 21524 df020109f1    837 (  0)  3.68 0.51 0.20   25 (116)   16 ( 50) 
C 20585 21605 ae040109r1    869 (  0)  0.95 0.95 0.11   31 ( 72)   47 ( 47) 
  20701 21692 eb050109f1    925 (  0)  0.41 0.52 0.00   27 ( 27)    0 (  0) 
  20705 21781 de070109f1    491 (  0)  0.58 0.58 0.00   44 ( 44)  519 (519) 
C 20717 21742 aa010109r1    712 (  0)  3.92 1.27 0.00  107 (268)   52 ( 52) 
  20713 21716 cf120109f1    491 (  0)  0.19 0.97 0.00   34 ( 29)  454 (454) 
C 20823 21834 ca010109r1    804 (  0)  1.68 0.89 0.11   69 (133)   49 ( 49) 
  20826 21831 da100109f1    862 (  0)  1.58 0.42 0.32   27 ( 27)   32 ( 66) 
C 20862 21904 de020109r1    847 (  0)  0.78 0.45 0.11   98 (137)   49 ( 49) 
C 20937 21881 ea110109r1    844 (  0)  1.22 0.22 0.11    0 ( 15)   47 ( 47) 
C 20970 21992 dc020109r1    853 (  0)  1.59 0.95 0.00   29 ( 29)   50 ( 50) 
  21044 22036 ca110109f1    859 (  0)  1.27 1.17 0.00   22 ( 89)   28 ( 36) 
  21099 22301 ab050109r1    741 (  0)  2.81 0.59 0.23  169 (169)  180 (195) 
C 21243 22242 cg010109r1    825 (  0)  1.31 1.41 0.00   30 ( 87)   51 ( 51) 
C 21557 22636 dc050109r1    840 (  0)  1.69 1.38 0.00   74 (127)   61 ( 61) 
C 21583 22606 cf020109r1    820 (  0)  1.68 2.11 0.00   21 (110)   53 ( 53) 
  21628 22658 ag060109f1    888 (  0)  1.32 1.12 0.10   25 ( 25)   24 ( 85) 
  21633 22675 bc010109r1    784 (  0)  0.71 0.95 0.00   47 ( 47)  156 (173) 
  21640 22651 ae100109r1    882 (  0)  1.15 1.04 0.00   47 ( 47)    5 ( 18) 
C 21640 22662 dh030109r1    817 (  0)  2.68 0.11 0.00   79 (138)   47 ( 47) 
  21695 22749 ad040109r1    878 (  0)  1.27 0.53 0.11   47 ( 46)   61 ( 76) 
  21803 22937 ab060109f1    841 (  0)  1.17 1.28 0.21  112 (112)   85 (157) 
  21973 22988 bg040109f1    837 (  0)  1.48 1.59 0.00   25 ( 25)   45 ( 83) 
  21975 23004 bb050109f1    888 (  0)  1.85 0.41 0.10   25 ( 25)   34 ( 51) 
  21976 22965 cb110109r1    862 (  0)  0.76 0.76 0.11   50 ( 50)   15 ( 20) 
  22022 23039 ad030109f1    875 (  0)  2.14 0.92 0.00   21 ( 21)   17 (103) 
  22077 23048 eh030109f1    926 (  0)  0.42 0.00 0.00   27 ( 27)    1 (  1) 
  22081 23069 ae110109f1    892 (  0)  1.37 0.21 0.00   24 ( 24)   19 ( 27) 
C 22121 23122 ac110109r1    879 (  0)  1.68 0.52 0.00    2 ( 37)   45 ( 45) 
C 22375 23356 eb050109r1    885 (  0)  0.75 0.32 0.11    2 (  9)   46 ( 46) 
  22389 23392 df010109r1    820 (  0)  1.67 0.56 0.00   49 ( 49)   59 ( 92) 
  22409 23455 be090109r1    891 (  0)  0.53 0.53 0.00   48 ( 47)   61 ( 61) 
  22576 23538 ba120109f1    767 (  0)  1.37 1.60 0.11   39 ( 39)   47 ( 68) 
  22613 23581 eg040109r1    849 (  0)  0.87 0.98 0.00   47 ( 47)    1 ( 12) 
  22667 23650 ab110109r1    828 (  0)  1.98 0.11 0.11   50 ( 50)   27 ( 42) 
C 22703 23832 ab050109f1    750 (  0)  2.00 0.59 0.12  175 (174)  105 (105) 
C 22727 23748 df020109r1    878 (  0)  1.65 0.41 0.10    4 ( 46)   50 ( 50) 
  22730 23807 bh070109r1    291 (  0)  4.74 0.56 0.00   85 ( 85)  634 (651) 
C 22768 23771 da100109r1    865 ( 31)  0.95 0.95 0.00   12 ( 68)   45 ( 45) 
C 22868 23854 cb110109f1    874 (  0)  0.74 0.53 0.32    9 ( 24)   29 ( 29) 
C 22878 23909 be090109f1    870 (  0)  1.21 1.51 0.20   11 ( 11)   30 ( 33) 
C 22900 23892 ca110109r1    850 (  0)  1.17 1.06 0.00    3 ( 34)   46 ( 46) 
C 22941 23989 ad040109f1    891 (  0)  1.90 0.50 0.20   18 ( 23)   32 ( 32) 
C 23056 24084 ad030109r1    868 (  0)  1.38 0.32 0.00   45 ( 77)   45 ( 45) 
  23066 24112 af060109r1    813 (  0)  1.44 0.55 0.22   47 ( 47)   99 (183) 
C 23171 24177 ab110109f1    836 (  0)  1.17 1.17 0.11   15 ( 15)   55 ( 55) 
C 23203 24227 db010109f1    857 (130)  2.46 0.51 0.10    5 (  5)   43 ( 43) 
C 23221 24242 ab060109r1    829 (  0)  1.86 1.44 0.10    7 ( 53)   46 ( 46) 
C 23219 24218 ae100109f1    906 (  0)  1.23 0.10 0.10    2 (  2)   25 ( 25) 
  23234 24306 ae070109r1    807 (  0)  1.61 1.40 0.00   60 ( 60)   84 (133) 
  23296 24333 db080109f1    871 ( 92)  1.60 1.10 0.10   25 ( 24)   11 ( 80) 
C 23306 24327 dh050109r1    759 (  0)  1.55 1.22 0.55   76 (108)   44 ( 44) 
C 23362 24369 bc010109f1    775 (  0)  1.24 1.13 0.11   93 ( 87)   27 ( 27) 
C 23423 24446 ag060109r1    845 (  0)  1.97 0.52 0.10   13 ( 33)   45 ( 45) 
C 23566 24525 eh030109r1    822 (  0)  0.55 0.77 0.00    0 (  0)   47 ( 47) 
  23585 24676 ab030109f1    787 (  0)  1.74 0.87 0.11   77 ( 77)   94 (159) 
C 23629 24619 ee080109f1    731 (  0)  1.47 0.37 0.00  154 (153)   22 ( 12) 
C 23664 24689 bg040109r1    786 (  0)  1.31 1.31 0.00   59 ( 75)   49 ( 49) 
C 23677 24712 bb050109r1    852 (  0)  1.41 1.21 0.00    0 ( 43)   46 ( 46) 
  23737 24723 ee080109r1    756 (  0)  0.37 0.12 0.25   46 ( 46)  126 (115) 
  23741 24769 bd050109f1    870 (  0)  1.42 0.71 0.00   25 ( 25)   15 ( 63) 
C 24174 25235 ae110109r1    803 (  0)  1.69 0.95 0.00    5 ( 66)  113 (113) 
  24209 25236 cd100109f1    858 (  0)  1.80 0.50 0.10   27 ( 27)    3 ( 46) 
C 24219 25192 eg040109f1    857 (  0)  0.84 0.21 0.11    0 (  9)   26 ( 26) 
C 24457 25437 ba120109r1    704 (  0)  2.28 0.72 0.12   81 (111)   65 ( 65) 
  24497 25541 cb060109f1    832 (  0)  1.05 0.42 0.52   24 ( 24)   66 (111) 
C 24577 25611 af060109f1    858 (  0)  0.93 0.52 0.10   45 ( 66)   25 ( 25) 
C 24578 25573 bh070109f1    755 (  0)  2.67 0.21 0.85   24 ( 63)   34 ( 34) 
C 24686 25834 ae070109f1    771 (  0)  0.43 2.17 0.00   96 (121)  131 (125) 
  24697 25709 bg050109f1    801 (  0)  1.18 1.18 0.00   30 ( 30)   50 ( 73) 
  24843 25870 ah050109r1    823 (  0)  0.97 0.54 0.00   48 ( 48)   56 ( 51) 
  24860 25840 ed100109r1    832 (  0)  1.19 0.33 0.00   55 ( 55)    4 (  4) 
  24879 25929 dc090109f1    828 (  0)  0.97 0.54 0.00   34 ( 34)   93 ( 73) 
  24965 25988 ba070109f1    765 (  0)  2.92 1.56 0.10   22 ( 22)   42 ( 71) 
C 25040 26060 ab030109r1    798 (  0)  1.98 0.22 0.11   65 ( 65)   47 ( 47) 
C 25105 26149 bd050109r1    822 (  0)  0.53 1.38 0.00   57 (102)   49 ( 49) 
  25137 26173 ag080109r1    806 (  0)  1.56 1.46 0.00   45 ( 45)   31 (145) 
C 25315 26356 db080109r1    804 (  0)  1.04 1.35 0.31   27 ( 81)   53 ( 53) 
  25383 26437 aa020109f1    197 (  0)  9.33 1.46 0.29   65 (141)  647 (669) 
  25601 26601 df120109r1    842 (  0)  1.26 0.53 0.00   51 ( 51)    0 ( 16) 
C 25906 26922 dc090109r1    834 (  0)  1.24 0.93 0.00    0 (  0)   50 ( 50) 
C 26038 27027 df120109f1    816 (  0)  1.65 1.14 0.00    0 ( 35)   22 ( 22) 
C 26042 27089 cb060109r1    809 (  0)  0.77 0.88 0.00   86 ( 85)   49 ( 49) 
  26134 27177 ad050109r1    848 (  0)  1.60 0.90 0.10   46 ( 46)    0 (  0) 
C 26245 27215 ed100109f1    878 (  0)  0.11 0.11 0.00    0 (  0)   23 ( 23) 
C 26335 27335 df010109f1    796 (  0)  1.44 1.54 0.10    0 ( 52)   28 ( 28) 
  26399 27357 ee020109r1    823 (  0)  0.44 0.11 0.00   50 ( 50)    0 (  0) 
C 26445 27469 ba070109r1    798 (  0)  1.85 0.72 0.21    2 ( 52)   48 ( 48) 
C 26654 27695 bg050109r1    720 (  0)  0.91 1.37 0.11  113 (191)   52 ( 52) 
C 26942 27955 ah050109f1    798 (  0)  0.64 0.54 0.21   56 ( 56)   24 ( 24) 
C 26948 27976 ag080109f1    841 (  0)  0.90 0.80 0.20    1 (  1)   31 ( 39) 
C 27051 28052 aa020109r1    739 (  0)  1.82 1.39 0.21   19 ( 25)   50 ( 50) 
  27669 28709 dd020109f1    784 (  0)  1.06 1.60 0.00   28 ( 28)   74 (134) 
C 27675 28694 de010109f1    804 (  0)  1.18 0.86 0.00   62 (128)   27 ( 27) 
C 27872 28907 cd100109r1    695 (  0)  3.04 0.58 0.12  132 (171)   48 ( 48) 
C 28013 28969 ee020109f1    850 (  0)  0.54 0.11 0.21    0 (  0)   26 ( 26) 
C 28031 29063 ad050109f1    880 (  0)  1.76 0.39 0.29   10 ( 10)    0 ( 28) 
  28101 29038 eh020109f1    856 (  0)  0.22 0.22 0.00   21 ( 21)    3 (  3) 

Overall discrep rates (%):             1.71 0.88 0.09

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90   25333  87.2   25333  87.2    0.00
 89      37   0.1   25370  87.3    0.00
 88      41   0.1   25411  87.4    0.00
 87      48   0.2   25459  87.6    0.00
 86      33   0.1   25492  87.7    0.00
 85      36   0.1   25528  87.8    0.00
 84      42   0.1   25570  88.0    0.00
 83      28   0.1   25598  88.1    0.00
 82      28   0.1   25626  88.2    0.00
 81     101   0.3   25727  88.5    0.00
 80      16   0.1   25743  88.6    0.00
 79      26   0.1   25769  88.7    0.00
 78      36   0.1   25805  88.8    0.00
 77      28   0.1   25833  88.9    0.00
 76      42   0.1   25875  89.0    0.00
 75      43   0.1   25918  89.2    0.00
 74      17   0.1   25935  89.2    0.00
 73      17   0.1   25952  89.3    0.00
 72      19   0.1   25971  89.4    0.00
 71       7   0.0   25978  89.4    0.00
 70       7   0.0   25985  89.4    0.00
 69       5   0.0   25990  89.4    0.00
 68      11   0.0   26001  89.5    0.00
 67       5   0.0   26006  89.5    0.00
 66    1580   5.4   27586  94.9    0.00
 65       3   0.0   27589  94.9    0.00
 63       1   0.0   27590  94.9    0.00
 62       2   0.0   27592  94.9    0.00
 61     262   0.9   27854  95.8    0.00
 60      35   0.1   27889  96.0    0.00
 59       1   0.0   27890  96.0    0.00
 58       5   0.0   27895  96.0    0.00
 57       3   0.0   27898  96.0    0.00
 56     531   1.8   28429  97.8    0.00
 55      27   0.1   28456  97.9    0.00
 54      30   0.1   28486  98.0    0.00
 53      81   0.3   28567  98.3    0.00
 52      47   0.2   28614  98.5    0.00
 51      90   0.3   28704  98.8    0.00
 50      37   0.1   28741  98.9    0.00
 49       6   0.0   28747  98.9    0.00
 48      14   0.0   28761  99.0    0.00
 47       9   0.0   28770  99.0    0.00
 46      13   0.0   28783  99.0    0.00
 45       4   0.0   28787  99.1    0.00
 44      21   0.1   28808  99.1    0.01
 43      19   0.1   28827  99.2    0.01
 42      26   0.1   28853  99.3    0.01
 41      10   0.0   28863  99.3    0.01
 40      16   0.1   28879  99.4    0.01
 38       1   0.0   28880  99.4    0.01
 37      20   0.1   28900  99.4    0.01
 36       1   0.0   28901  99.4    0.02
 35       6   0.0   28907  99.5    0.02
 34       3   0.0   28910  99.5    0.02
 33       4   0.0   28914  99.5    0.02
 32       7   0.0   28921  99.5    0.02
 30       2   0.0   28923  99.5    0.03
 29       9   0.0   28932  99.5    0.04
 27       2   0.0   28934  99.6    0.04
 26       2   0.0   28936  99.6    0.05
 25       1   0.0   28937  99.6    0.05
 24       2   0.0   28939  99.6    0.06
 19       1   0.0   28940  99.6    0.07
 16       1   0.0   28941  99.6    0.10
 15       1   0.0   28942  99.6    0.13
 14       2   0.0   28944  99.6    0.21
 13       2   0.0   28946  99.6    0.31
 12       1   0.0   28947  99.6    0.37
 11       5   0.0   28952  99.6    0.77
  9       2   0.0   28954  99.6    1.02
 -1     109   0.4   29063 100.0  110.02   (quality -1 = terminal quality 0)

Avg. full length: 29063.0, trimmed (qual > -1): 28954.0
Avg. quality: 86.4 per base

Initial, terminal qual 0 segments:  1-81, 29036-29063

Regions of LLR- adjusted quality < 2.0:
1-84, 28981-28985, 29029-29063, 

3 regions, avg size 41.3, avg spacing 9687.7

First_start: 104, last_end: 29035
 Unused pair: ab020109f1 dd100109r1  0.0   0
LLR breakdown: discreps: -0.2 (<20 part: -0.2 (#=5), >20:0.0 (#=0); in HQ: 0.0, out HQ -0.2), match: 0.9  trail: -0.1  lead: 0.0  total: 0.6   32 10.42 0.00 0.00  ab020109f1       29    76 (968)  C dd100109r1   (944)    95    48  
 Unused pair: cb080109f1 eh040109r1  5.8   2
LLR breakdown: discreps: -0.7 (<20 part: -0.7 (#=10), >20:0.0 (#=0); in HQ: -0.2, out HQ -0.5), match: 7.1  trail: 0.0  lead: 0.0  total: 6.4  285  1.55 1.55 0.00  cb080109f1       24   346 (710)  C eh040109r1   (598)   375    48 *
 Unused pair: ac020109f1 eh040109r1  8.1   1
LLR breakdown: discreps: -1.9 (<20 part: -1.9 (#=14), >20:0.0 (#=0); in HQ: -1.1, out HQ -0.8), match: 9.3  trail: 0.0  lead: 0.0  total: 7.4  377  2.34 0.70 0.23  ac020109f1       30   457 (604)  C eh040109r1   (496)   477    48 *
 Unused pair: bh060109f1 eh040109r1  8.4   0
LLR breakdown: discreps: -1.3 (<20 part: -1.3 (#=13), >20:0.0 (#=0); in HQ: -1.0, out HQ -0.3), match: 9.2  trail: 0.0  lead: 0.0  total: 7.9  376  1.64 1.17 0.23  bh060109f1       22   447 (556)  C eh040109r1   (496)   477    48 *
 Unused pair: cb010109f1 eh040109r1  -14.3   0
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=6), >20:0.0 (#=0); in HQ: -0.2, out HQ -0.3), match: 10.6  trail: 0.0  lead: -24.2  total: -14.1  452  0.63 0.63 0.00  cb010109f1      177   654 (383)  C eh040109r1   (445)   528    48 *
 Unused pair: cd050109f1 eh040109r1  -14.3   2
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=6), >20:0.0 (#=0); in HQ: -0.2, out HQ -0.3), match: 10.6  trail: 0.0  lead: -24.2  total: -14.1  452  0.63 0.63 0.00  cd050109f1      263   740 (309)  C eh040109r1   (445)   528    48 *
 Unused pair: dh060109f1 eh040109r1  -2.1   4
LLR breakdown: discreps: -2.9 (<20 part: -0.7 (#=8), >20:-2.2 (#=1); in HQ: -2.4, out HQ -0.5), match: 10.5  trail: -13.1  lead: 0.0  total: -5.5  442  1.04 0.63 0.21  dh060109f1      307   785 (253)    eh040109r1       48   528 (445) *
 Unused pair: af100109f1 eh040109r1  -4.9   2
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=6), >20:0.0 (#=0); in HQ: -0.2, out HQ -0.3), match: 10.6  trail: -14.8  lead: 0.0  total: -4.7  452  0.63 0.63 0.00  af100109f1      262   739 (290)    eh040109r1       48   528 (445) *
 Unused pair: ef110109f1 eh040109r1  -14.3   0
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=6), >20:0.0 (#=0); in HQ: -0.2, out HQ -0.3), match: 10.6  trail: 0.0  lead: -24.2  total: -14.1  452  0.63 0.63 0.00  ef110109f1      225   702 (253)  C eh040109r1   (445)   528    48 *
 Unused pair: bh020109f1 eh040109r1  -14.4   2
LLR breakdown: discreps: -1.2 (<20 part: -1.2 (#=12), >20:0.0 (#=0); in HQ: -0.8, out HQ -0.4), match: 10.5  trail: 0.0  lead: -24.2  total: -14.9  439  2.08 0.21 0.21  bh020109f1      298   778 (243)  C eh040109r1   (445)   528    48 *
 Unused pair: ah110109f1 eh040109r1  -14.3   0
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=6), >20:0.0 (#=0); in HQ: -0.2, out HQ -0.3), match: 10.6  trail: 0.0  lead: -24.2  total: -14.1  452  0.63 0.63 0.00  ah110109f1      291   768 (228)  C eh040109r1   (445)   528    48 *
 Unused pair: bf110109f1 eh040109r1  -14.3   2
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=6), >20:0.0 (#=0); in HQ: -0.2, out HQ -0.3), match: 10.6  trail: -24.2  lead: 0.0  total: -14.1  452  0.63 0.63 0.00  bf110109f1      138   615 (380)    eh040109r1       48   528 (445) *
 Unused pair: ac120109r1 eh040109r1  -14.3   2
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=6), >20:0.0 (#=0); in HQ: -0.2, out HQ -0.3), match: 10.6  trail: -24.2  lead: 0.0  total: -14.1  452  0.63 0.63 0.00  ac120109r1      132   609 (393)    eh040109r1       48   528 (445) *
 Unused pair: cg040109f1 eh040109r1  -14.4   1
LLR breakdown: discreps: -0.2 (<20 part: -0.2 (#=6), >20:0.0 (#=0); in HQ: 0.0, out HQ -0.2), match: 9.8  trail: 0.0  lead: -24.2  total: -14.6  421  1.12 0.22 0.00  cg040109f1      467   911 (144)  C eh040109r1   (445)   528    83  
 Unused pair: ba010109f1 eh040109r1  -14.4   2
LLR breakdown: discreps: -1.1 (<20 part: -1.1 (#=18), >20:0.0 (#=0); in HQ: 0.0, out HQ -1.1), match: 10.2  trail: -0.2  lead: -24.2  total: -15.3  413  2.94 0.21 0.63  ba010109f1      468   944 (68)  C eh040109r1   (445)   528    54 *
 Unused pair: eh040109r1 eh070109r1  -14.3   1
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=6), >20:0.0 (#=0); in HQ: -0.2, out HQ -0.3), match: 10.6  trail: -24.2  lead: 0.0  total: -14.1  453  0.62 0.00 0.62  eh040109r1       48   528 (445)    eh070109r1      288   765 (215) *
 Unused pair: cb050109f1 eh040109r1  -17.0   1
LLR breakdown: discreps: -1.4 (<20 part: -1.4 (#=15), >20:0.0 (#=0); in HQ: -0.1, out HQ -1.3), match: 7.2  trail: 0.0  lead: -24.2  total: -18.4  278  3.26 0.00 1.19  cb050109f1      676  1012 (119)  C eh040109r1   (445)   528   196 *
 Unused pair: dh070109f1 eh040109r1  -18.8   1
LLR breakdown: discreps: -0.6 (<20 part: -0.6 (#=14), >20:0.0 (#=0); in HQ: 0.0, out HQ -0.6), match: 5.0  trail: 0.0  lead: -24.2  total: -19.8  190  1.96 0.00 3.53  dh070109f1      750  1004 (143)  C eh040109r1   (445)   528   283 *
 Unused pair: ah100109r1 eh040109r1  -21.0   3
LLR breakdown: discreps: -0.2 (<20 part: -0.2 (#=2), >20:0.0 (#=0); in HQ: -0.2, out HQ 0.0), match: 3.2  trail: -24.2  total: -21.2  133  1.39 0.00 0.00  ah100109r1      145   288 (863)    eh040109r1      385   528 (445)  
 Unused pair: ca050109r1 eh040109r1  -12.0   1
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=15), >20:0.0 (#=0); in HQ: 0.0, out HQ -0.5), match: 2.2  trail: 0.0  lead: -15.0  total: -13.3   88  7.48 0.00 2.72  ca050109r1      816   962 (100)  C eh040109r1   (445)   528   386 *
 Unused pair: cc040109f1 eh040109r1  -20.8   2
LLR breakdown: discreps: -0.4 (<20 part: -0.4 (#=6), >20:0.0 (#=0); in HQ: -0.4, out HQ 0.0), match: 3.7  trail: -24.2  lead: 0.0  total: -20.9  151  2.86 0.00 0.57  cc040109f1       39   213 (865)    eh040109r1      355   528 (445) *

Slack, # used pairs (max_score), unused
 0   932  (21.1)     5 ( 8.4)     4394
 1  1260  (21.0)     6 ( 8.1)      453
 2   817  (21.5)     8 ( 5.8)        4
 3   471  (20.9)     1 (-21.0)        0
 4   277  (20.0)     1 (-2.1)        0
 5   166  (20.5)     0 ( 0.0)        0
 6   144  (20.2)     0 ( 0.0)        0
 7   114  (19.1)     0 ( 0.0)        0
 8    85  (19.5)     0 ( 0.0)        0
 9    60  (19.0)     0 ( 0.0)        0
10    30  (19.1)     0 ( 0.0)        0
11    21  (19.6)     0 ( 0.0)        0
12    12  (17.3)     0 ( 0.0)        0
13    10  (17.5)     0 ( 0.0)        0
14     4  (14.0)     0 ( 0.0)        0
15     3  (15.9)     0 ( 0.0)        0
16     1  (12.3)     0 ( 0.0)        0
17     1  ( 0.0)     0 ( 0.0)        0
26     1  ( 0.0)     0 ( 0.0)        0
29     1  ( 0.0)     0 ( 0.0)        0
99     9  (10.0)   411 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
27358 - 27696      339       ee020109r1   (26399)    No           1298
29036 - right       28+      eh020109f1   (28101)    No            962+

Bottom strand: 
 left -  2410     2410+      dg120109r1   (3400)    No           3400+
29064 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56  88934  88934 348833 (100.00)    71  0    0   0   0   0     0 (0.00)    0  9175 (2.63)
51  19190 108124 259899 ( 74.51)    23  0    0   0   0   0     0 (0.00)    0  9175 (3.53)
50  14444 122568 240709 ( 69.00)    39  0    0   0   0   0     0 (0.00)    0  9175 (3.81)
48   1384 123952 226265 ( 64.86)    36  0    0   0   0   0     0 (0.00)    0  9175 (4.05)
47   2375 126327 224881 ( 64.47)     6  0    0   0   0   0     0 (0.00)    0  9175 (4.08)
46   4358 130685 222506 ( 63.79)    27  0    0   0   0   0     0 (0.00)    0  9175 (4.12)
45   3770 134455 218148 ( 62.54)     4  0    0   0   0   0     0 (0.00)    0  9175 (4.21)
44  10709 145164 214378 ( 61.46)    45  0    0   0   0   0     0 (0.00)    0  9175 (4.28)
43   8425 153589 203669 ( 58.39)    11  0    0   0   0   0     0 (0.00)    0  9175 (4.50)
42  22037 175626 195244 ( 55.97)    80  0    0   0   0   0     0 (0.00)    0  9175 (4.70)
41   2298 177924 173207 ( 49.65)    10  0    0   0   0   0     0 (0.00)    0  9175 (5.30)
40  16235 194159 170909 ( 48.99)   169  0    0   0   0   0     0 (0.00)    0  9175 (5.37)
39    601 194760 154674 ( 44.34)    17  0    0   0   0   0     0 (0.00)    0  9175 (5.93)
38   1289 196049 154073 ( 44.17)     7  0    0   0   0   0     0 (0.00)    0  9175 (5.95)
37   7440 203489 152784 ( 43.80)    47  0    0   0   0   0     0 (0.00)    0  9175 (6.01)
36    724 204213 145344 ( 41.67)     6  0    0   0   0   0     0 (0.00)    0  9175 (6.31)
35   6286 210499 144620 ( 41.46)    45  0    0   0   1   0     1 (0.02)    1  9175 (6.34)
34   2877 213376 138334 ( 39.66)    24  0    0   0   0   0     0 (0.00)    1  9174 (6.63)
33   3556 216932 135457 ( 38.83)    26  0    0   0   0   0     0 (0.00)    1  9174 (6.77)
32   3229 220161 131901 ( 37.81)    65  0    0   0   2   0     2 (0.06)    3  9174 (6.96)
31   1597 221758 128672 ( 36.89)    15  0    0   0   0   0     0 (0.00)    3  9172 (7.13)
30   1738 223496 127075 ( 36.43)    26  0    0   0   0   0     0 (0.00)    3  9172 (7.22)
29   6844 230340 125337 ( 35.93)   167  0    0   0  12   1    13 (0.19)   16  9172 (7.32)
28   2015 232355 118493 ( 33.97)    19  0    0   0   1   0     1 (0.05)   17  9159 (7.73)
27   2922 235277 116478 ( 33.39)    81  0    0   0   4   1     5 (0.17)   22  9158 (7.86)
26   1245 236522 113556 ( 32.55)    68  0    0   2   1   1     4 (0.32)   26  9153 (8.06)
25   4049 240571 112311 ( 32.20)   116  0    0   3   5   0     8 (0.20)   34  9149 (8.15)
24   2926 243497 108262 ( 31.04)   109  0    0   0   3   1     4 (0.14)   38  9141 (8.44)
23   2479 245976 105336 ( 30.20)   125  0    0   2   7   0     9 (0.36)   47  9137 (8.67)
22   2105 248081 102857 ( 29.49)    97  0    0   3   4   0     7 (0.33)   54  9128 (8.87)
21   2977 251058 100752 ( 28.88)   132  0    0   8   8   1    17 (0.57)   71  9121 (9.05)
20   2639 253697  97775 ( 28.03)   157  0    0   1   7   1     9 (0.34)   80  9104 (9.31)
19   3829 257526  95136 ( 27.27)   277  0    0   7  12   0    19 (0.50)   99  9095 (9.56)
18   3087 260613  91307 ( 26.17)   141  0    0  14  12   0    26 (0.84)  125  9076 (9.94)
17   2952 263565  88220 ( 25.29)   172  0    0  23  20   0    43 (1.46)  168  9050 (10.26)
16   3192 266757  85268 ( 24.44)   211  0    0  29  17   2    48 (1.50)  216  9007 (10.56)
15   4583 271340  82076 ( 23.53)   263  0    0  46  25   5    76 (1.66)  292  8959 (10.92)
14   3770 275110  77493 ( 22.21)   224  0    0  73  18   6    97 (2.57)  389  8883 (11.46)
13   5311 280421  73723 ( 21.13)   375  0    0 139  41  11   191 (3.60)  580  8786 (11.92)
12   5612 286033  68412 ( 19.61)   387  0    0 147  89  13   249 (4.44)  829  8595 (12.56)
11   8076 294109  62800 ( 18.00)   483  0    0 426 108  26   560 (6.93)  1389  8346 (13.29)
10   9950 304059  54724 ( 15.69)   768  0    0 532 213  39   784 (7.88)  2173  7786 (14.23)
 9  16526 320585  44774 ( 12.84)  1466  0    0 1092 433 110   1635 (9.89)  3808  7002 (15.64)
 8  11874 332459  28248 (  8.10)  1220  0    0 1170 617  62   1849 (15.57)  5657  5367 (19.00)
 7  10628 343087  16374 (  4.69)   860  0    0 1316 722  27   2065 (19.43)  7722  3518 (21.49)
 6   5169 348256   5746 (  1.65)   814  0    0 660 532  18   1210 (23.41)  8932  1453 (25.29)
 4    489 348745    577 (  0.17)    61  0    0 140  19   1   160 (32.72)  9092  243 (42.11)
 0     88 348833     88 (  0.03)   685  0   58   0  24   1    83 (94.32)  9175   83 (94.32)
-1    312 349145      0 (  0.00)  37654  0    0  19  33   1    53 (16.99)  9228    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90 273430 273430 335352 (100.00)     8  0    0   0   0   0     0 (0.00)    0  6398 (1.91)
89    232 273662  61922 ( 18.46)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.33)
88    222 273884  61690 ( 18.40)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.37)
87    324 274208  61468 ( 18.33)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.41)
86    230 274438  61144 ( 18.23)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.46)
85    210 274648  60914 ( 18.16)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.50)
84    214 274862  60704 ( 18.10)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.54)
83    122 274984  60490 ( 18.04)     1  0    0   0   0   0     0 (0.00)    0  6398 (10.58)
82    181 275165  60368 ( 18.00)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.60)
81    957 276122  60187 ( 17.95)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.63)
80     58 276180  59230 ( 17.66)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.80)
79    123 276303  59172 ( 17.64)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.81)
78    134 276437  59049 ( 17.61)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.84)
77     77 276514  58915 ( 17.57)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.86)
76    260 276774  58838 ( 17.55)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.87)
75    110 276884  58578 ( 17.47)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.92)
74     37 276921  58468 ( 17.43)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.94)
73    134 277055  58431 ( 17.42)     1  0    0   0   0   0     0 (0.00)    0  6398 (10.95)
72     56 277111  58297 ( 17.38)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.97)
71     96 277207  58241 ( 17.37)     0  0    0   0   0   0     0 (0.00)    0  6398 (10.99)
70     30 277237  58145 ( 17.34)     1  0    0   0   0   0     0 (0.00)    0  6398 (11.00)
69     90 277327  58115 ( 17.33)     0  0    0   0   0   0     0 (0.00)    0  6398 (11.01)
68     78 277405  58025 ( 17.30)     0  0    0   0   0   0     0 (0.00)    0  6398 (11.03)
67    163 277568  57947 ( 17.28)     1  0    0   0   0   0     0 (0.00)    0  6398 (11.04)
66   5621 283189  57784 ( 17.23)     1  0    0   0   1   0     1 (0.02)    1  6398 (11.07)
65    707 283896  52163 ( 15.55)     1  0    0   0   0   0     0 (0.00)    1  6397 (12.26)
64     36 283932  51456 ( 15.34)     1  0    0   0   0   0     0 (0.00)    1  6397 (12.43)
63     15 283947  51420 ( 15.33)     0  0    0   0   0   0     0 (0.00)    1  6397 (12.44)
62    156 284103  51405 ( 15.33)     0  0    0   0   0   0     0 (0.00)    1  6397 (12.44)
61    831 284934  51249 ( 15.28)     1  0    0   0   0   0     0 (0.00)    1  6397 (12.48)
60    273 285207  50418 ( 15.03)     0  0    0   0   0   0     0 (0.00)    1  6397 (12.69)
59    162 285369  50145 ( 14.95)     0  0    0   0   0   0     0 (0.00)    1  6397 (12.76)
58    180 285549  49983 ( 14.90)     1  0    0   0   0   0     0 (0.00)    1  6397 (12.80)
57    334 285883  49803 ( 14.85)     3  0    0   0   0   0     0 (0.00)    1  6397 (12.84)
56    949 286832  49469 ( 14.75)    23  0    0   0   0   0     0 (0.00)    1  6397 (12.93)
55    157 286989  48520 ( 14.47)     0  0    0   0   0   0     0 (0.00)    1  6397 (13.18)
54    576 287565  48363 ( 14.42)     0  0    0   0   0   0     0 (0.00)    1  6397 (13.23)
53    352 287917  47787 ( 14.25)     0  0    0   0   0   0     0 (0.00)    1  6397 (13.39)
52    479 288396  47435 ( 14.14)     5  0    0   0   0   0     0 (0.00)    1  6397 (13.49)
51    268 288664  46956 ( 14.00)     2  0    0   0   1   0     1 (0.37)    2  6397 (13.62)
50    389 289053  46688 ( 13.92)    16  0    0   0   1   0     1 (0.26)    3  6396 (13.70)
49    295 289348  46299 ( 13.81)     0  0    0   0   0   0     0 (0.00)    3  6395 (13.81)
48    314 289662  46004 ( 13.72)     1  0    0   0   0   0     0 (0.00)    3  6395 (13.90)
47    171 289833  45690 ( 13.62)     3  0    0   0   2   0     2 (1.17)    5  6395 (14.00)
46    379 290212  45519 ( 13.57)     2  0    0   0   0   0     0 (0.00)    5  6393 (14.04)
45    331 290543  45140 ( 13.46)     4  0    0   0   0   0     0 (0.00)    5  6393 (14.16)
44    504 291047  44809 ( 13.36)    10  0    0   0   0   0     0 (0.00)    5  6393 (14.27)
43    346 291393  44305 ( 13.21)     7  0    0   0   0   0     0 (0.00)    5  6393 (14.43)
42    501 291894  43959 ( 13.11)    20  0    0   0   0   0     0 (0.00)    5  6393 (14.54)
41    503 292397  43458 ( 12.96)     5  0    0   0   0   0     0 (0.00)    5  6393 (14.71)
40  10884 303281  42955 ( 12.81)    17  0    0   0   0   0     0 (0.00)    5  6393 (14.88)
39     72 303353  32071 (  9.56)     2  0    0   0   1   0     1 (1.39)    6  6393 (19.93)
38     57 303410  31999 (  9.54)     0  0    0   0   0   0     0 (0.00)    6  6392 (19.98)
37    124 303534  31942 (  9.52)     9  0    0   0   0   0     0 (0.00)    6  6392 (20.01)
36     88 303622  31818 (  9.49)     4  0    0   0   1   0     1 (1.14)    7  6392 (20.09)
35    177 303799  31730 (  9.46)     8  0    0   0   1   0     1 (0.56)    8  6391 (20.14)
34    252 304051  31553 (  9.41)     8  0    0   0   2   0     2 (0.79)   10  6390 (20.25)
33    198 304249  31301 (  9.33)     7  0    0   0   0   0     0 (0.00)   10  6388 (20.41)
32    195 304444  31103 (  9.27)     7  0    0   0   3   0     3 (1.54)   13  6388 (20.54)
31     99 304543  30908 (  9.22)     4  0    0   1   0   0     1 (1.01)   14  6385 (20.66)
30     63 304606  30809 (  9.19)     4  0    0   1   0   0     1 (1.59)   15  6384 (20.72)
29    209 304815  30746 (  9.17)    35  0    0   0  12   1    13 (6.22)   28  6383 (20.76)
28     80 304895  30537 (  9.11)     5  0    0   1   2   0     3 (3.75)   31  6370 (20.86)
27    214 305109  30457 (  9.08)    19  0    0   0   7   1     8 (3.74)   39  6367 (20.90)
26     97 305206  30243 (  9.02)    12  0    0   1   1   1     3 (3.09)   42  6359 (21.03)
25    629 305835  30146 (  8.99)    20  0    0   4   4   0     8 (1.27)   50  6356 (21.08)
24    309 306144  29517 (  8.80)    13  0    0   3   5   2    10 (3.24)   60  6348 (21.51)
23    281 306425  29208 (  8.71)    16  0    0   2  14   0    16 (5.69)   76  6338 (21.70)
22    192 306617  28927 (  8.63)     8  0    0   3   7   0    10 (5.21)   86  6322 (21.86)
21    278 306895  28735 (  8.57)    15  0    0   7   9   1    17 (6.12)  103  6312 (21.97)
20    264 307159  28457 (  8.49)    13  0    0   1   7   1     9 (3.41)  112  6295 (22.12)
19    486 307645  28193 (  8.41)    27  0    0   7  12   0    19 (3.91)  131  6286 (22.30)
18    265 307910  27707 (  8.26)    15  0    0   9  10   0    19 (7.17)  150  6267 (22.62)
17    410 308320  27442 (  8.18)    21  0    0  16  16   1    33 (8.05)  183  6248 (22.77)
16    550 308870  27032 (  8.06)    20  0    0  25  16   2    43 (7.82)  226  6215 (22.99)
15    730 309600  26482 (  7.90)    30  0    0  42  34   8    84 (11.51)  310  6172 (23.31)
14    628 310228  25752 (  7.68)    29  0    0  49  12   6    67 (10.67)  377  6088 (23.64)
13   1224 311452  25124 (  7.49)    35  0    0 106  30  11   147 (12.01)  524  6021 (23.97)
12   1220 312672  23900 (  7.13)    28  0    0 103  65  12   180 (14.75)  704  5874 (24.58)
11   2274 314946  22680 (  6.76)    43  0    0 309  70  23   402 (17.68)  1106  5694 (25.11)
10   3048 317994  20406 (  6.08)    65  0    0 390 164  36   590 (19.36)  1696  5292 (25.93)
 9   5681 323675  17358 (  5.18)    81  0    0 711 250  91   1052 (18.52)  2748  4702 (27.09)
 8   4467 328142  11677 (  3.48)    67  0    0 819 399  49   1267 (28.36)  4015  3650 (31.26)
 7   4436 332578   7210 (  2.15)    45  0    0 929 474  19   1422 (32.06)  5437  2383 (33.05)
 6   2332 334910   2774 (  0.83)    43  0    0 437 327  15   779 (33.40)  6216  961 (34.64)
 4    378 335288    442 (  0.13)    36  0    0 102  17   1   120 (31.75)  6336  182 (41.18)
 0     64 335352     64 (  0.02)    13  0   45   0  17   0    62 (96.88)  6398   62 (96.88)
-1  13793 349145      0 (  0.00)  46989  0   13 1774 996  47   2830 (20.52)  9228    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     109      109        2
  9       2      111        3
 11       5      116        5
 12       1      117        5
 13       2      119        4
 14       2      121        3
 15       1      122        3
 16       1      123        3
 19       1      124        3
 24       2      126        3
 25       1      127        3
 26       2      129        3
 27       2      131        4
 29       9      140        6
 30       2      142        7
 32       7      149        8
 33       4      153        9
 34       3      156       11
 35       6      162       11
 36       1      163       11
 37      20      183       15
 38       1      184       15
 40      16      200       17
 41      10      210       19
 42      26      236       23
 43      19      255       27
 44      21      276       30
 45       4      280       30
 46      13      293       30
 47       9      302       32
 48      14      316       33
 49       6      322       32
 50      37      359       42
 51      90      449       54
 52      47      496       70
 53      81      577       96
 54      30      607      104
 55      27      634      105
 56     531     1165       89
 57       3     1168       88
 58       5     1173       85
 59       1     1174       84
 60      35     1209       94
 61     262     1471      104
 62       2     1473      104
 63       1     1474      105
 65       3     1477      107
 66    1580     3057       17
 67       5     3062       18
 68      11     3073       24
 69       5     3078       27
 70       7     3085       30
 71       7     3092       32
 72      19     3111       35
 73      17     3128       44
 74      17     3145       46
 75      43     3188       54
 76      42     3230       58
 77      28     3258       64
 78      36     3294       72
 79      26     3320       76
 80      16     3336       70
 81     101     3437       86
 82      28     3465       87
 83      28     3493       90
 84      42     3535       91
 85      36     3571       91
 86      33     3604       94
 87      48     3652      109
 88      41     3693      112
 89      37     3730      119
 90   25333    29063        1

SS region: 2777 (9.56%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
 4558     -4.0  [-4.0,  0.0]  (0, 1)
 4873     -3.5  [-3.5,  0.0]  (0, 1)
 5657     -4.0  [-4.0,  0.0]  (0, 1)
 6228     -3.8  [-2.1,  0.0]  (1, 1)
 6802     -3.7  [-3.7,  0.0]  (0, 1)
 6895     -4.0  [-4.0,  0.0]  (0, 1)
 6898     -3.2  [-3.2,  0.0]  (1, 0)
 7541     -4.0  [-4.0,  0.0]  (0, 1)
 8056     -4.2  [-4.2,  0.0]  (0, 1)
 8152     -3.3  [-3.3,  0.0]  (0, 1)
 8418     -3.7  [-3.7,  0.0]  (0, 1)
 8472     -3.2  [-3.2,  0.0]  (0, 1)
 9540     -4.8  [-4.8,  0.0]  (0, 1)
11041     -3.8  [-2.0,  0.0]  (0, 2)
12911     -3.5  [-3.5,  0.0]  (1, 0)
14295     -5.6  [-5.6,  0.0]  (0, 1)
14777     -3.4  [-3.4,  0.0]  (0, 1)
14957     -4.0  [-4.0,  0.0]  (0, 1)
15672     -3.7  [-3.7,  0.0]  (0, 1)
16113     -3.9  [-2.2,  0.0]  (0, 2)
16535     -4.2  [-4.2,  0.0]  (0, 1)
17158     -3.2  [-3.2,  0.0]  (1, 0)
17538     -3.4  [-3.4,  0.0]  (0, 1)
18867     -4.3  [-2.5,  0.0]  (1, 1)
19135     -4.0  [-4.0,  0.0]  (0, 1)
19789     -4.0  [-4.0,  0.0]  (0, 1)
20517     -3.7  [-3.7,  0.0]  (0, 1)
20561     -4.0  [-4.0,  0.0]  (0, 1)
20725     -4.0  [-4.0,  0.0]  (0, 1)
21082     -4.0  [-4.0,  0.0]  (0, 1)
21137     -3.6  [-3.6,  0.0]  (0, 1)
21424     -5.1  [-5.1,  0.0]  (0, 1)
21856     -4.0  [-4.0,  0.0]  (0, 1)
22192     -4.0  [-4.0,  0.0]  (0, 1)
22554     -3.2  [-3.2,  0.0]  (0, 1)
22576     -3.7  [-3.7,  0.0]  (0, 1)
23699     -3.7  [-3.7,  0.0]  (0, 1)
23727     -3.7  [-3.7,  0.0]  (0, 1)
24040     -4.0  [-4.0,  0.0]  (0, 1)
24197     -3.5  [-3.5,  0.0]  (0, 1)
24284     -3.7  [-3.7,  0.0]  (0, 1)
24402     -4.0  [-4.0,  0.0]  (0, 1)
24641     -5.6  [-5.6,  0.0]  (0, 1)
25123     -3.5  [-3.5,  0.0]  (0, 1)
26304     -4.0  [-4.0,  0.0]  (0, 1)
26873     -4.0  [-4.0,  0.0]  (0, 1)
27041     -3.5  [-3.5,  0.0]  (0, 1)
28860     -4.0  [-4.0,  0.0]  (0, 1)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(16, 16)  3710- 3961 [-12.5] (0,0)   C dd100109r1         297-46 | (1 46)  46 313 | CHIMERIC || local(+/-) (5.5,5.1), distant (0.0,0.0)
LLR breakdown: discreps: -0.1 (<20 part: -0.1 (#=3), >20:0.0 (#=0); in HQ: -0.1, out HQ 0.0), match: 5.5  lead: -18.0  total: -12.6 
(0, 16)  3710- 3960 [-3.7] (0,0)     dd100109f1         30-280 | 14 280  (991 1045) | DU:(991 1045) [991 1045  with   ag040109f1  880 935]  CHIMERIC || local(+/-) (5.2,5.1), distant (1.1,0.0)
LLR breakdown: discreps: -0.2 (<20 part: -0.2 (#=2), >20:0.0 (#=0); in HQ: 0.0, out HQ -0.2), match: 5.6  trail: 0.0  lead: -9.1  total: -3.7 
(0, 254)   315-  322 [-3.0] (0,208)     da070109r1         360-367 || local(+/-) (10.0,0.0), distant (0.0,0.0)
LLR breakdown: discreps: 0.0 (<20 part: 0.0 (#=0), >20:0.0 (#=0); in HQ: 0.0, out HQ 0.0), match: 0.2  trail: -1.8  lead: -1.4  total: -3.0 
(13, 0)  5048- 5880 [16.7] (0,0)     cd110109r1         148-988 | (111 148)  148 1144 | DU:(**111 147**) [111 148  with   da100109r1  8 45]  CHIMERIC || local(+/-) (20.0,6.9), distant (0.3,0.0)
(0, 0)  5403- 6249 [-10.7] (0,0)     eg120109f1         39-896 || local(+/-) (14.5,0.0), distant (5.4,0.0)
LLR breakdown: discreps: -24.3 (<20 part: -24.3 (#=197), >20:0.0 (#=0); in HQ: 0.0, out HQ -24.3), match: 13.6  trail: 0.0  lead: 0.0  total: -10.7 
(0, 0)  6537- 7390 [-15.4] (0,0)   C eg120109r1         926-55 || local(+/-) (12.2,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -25.3 (<20 part: -25.3 (#=214), >20:0.0 (#=0); in HQ: 0.0, out HQ -25.3), match: 9.9  trail: 0.0  lead: 0.0  total: -15.4 
Bypassed: (0, 0) 12567-13044 [-14.1] (16,16)     eh040109r1         48-528 || local(+/-) (9.7,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=6), >20:0.0 (#=0); in HQ: -0.2, out HQ -0.3), match: 10.6  trail: -24.2  lead: 0.0  total: -14.1 
(12, 0) 12901-13766 [15.5] (0,0)     ah100109r1         145-1028 | (67 147)  145 1028 | DU:(**67 142**) [67 147  with   ab040109r1  4 85]  CHIMERIC || local(+/-) (16.9,0.0), distant (0.0,0.0)
(0, 0) 13761-14408 [-0.5] (0,0)     ac100109r1         218-867 || local(+/-) (9.1,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -8.4 (<20 part: -8.4 (#=106), >20:0.0 (#=0); in HQ: -2.7, out HQ -5.7), match: 7.9  trail: 0.0  lead: 0.0  total: -0.5 
(0, 0) 17529-18481 [18.2] (8,0)   C ad090109r1         1125-164 | (87 165)  164 1125 | DU:(**87 162**) [87 165  with   cc060109r1  39 117]  CHIMERIC || local(+/-) (19.8,4.1), distant (1.9,0.0)
(0, 0) 17786-18276 [-5.4] (16,9)     bd030109r1         49-540 || local(+/-) (11.0,0.0), distant (0.0,0.0)
LLR breakdown: discreps: 0.0 (<20 part: 0.0 (#=1), >20:0.0 (#=0); in HQ: 0.0, out HQ 0.0), match: 10.9  trail: -16.4  lead: 0.0  total: -5.5 
(0, 0) 19851-20162 [-2.7] (0,9)   C ec070109f1         340-26 || local(+/-) (6.5,6.4), distant (0.0,0.0)
LLR breakdown: discreps: -0.4 (<20 part: -0.4 (#=6), >20:0.0 (#=0); in HQ: -0.3, out HQ -0.1), match: 6.9  trail: -9.2  lead: 0.0  total: -2.7 
(0, 0) 19575-20505 [17.3] (9,0)   C ae120109r1         1085-147 | (115 150)  147 1091 | DU:(**115 146**) [115 150  with   dg010109r1  15 49]  [115 146  with   ad010109r1  26 57]  CHIMERIC || local(+/-) (20.1,6.5), distant (0.0,0.0)
(0, 0) 19882-19889 [ 0.0] (0,1389)   C bg070109r1         1470-1463 | 45 111 | LU:(45 90)(101 105) || local(+/-) (0.0,0.0), distant (0.0,0.0)
(0, 0) 19851-20162 [-11.2] (16,9)     ec070109r1         51-363 || local(+/-) (6.5,6.4), distant (0.0,0.0)
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=5), >20:0.0 (#=0); in HQ: -0.5, out HQ 0.0), match: 6.9  trail: -17.6  lead: 0.0  total: -11.2 
(16, 5) 20747-21263 [-2.2] (0,0)   C de070109r1         565-49 || local(+/-) (10.6,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -0.3 (<20 part: -0.3 (#=1), >20:0.0 (#=0); in HQ: -0.3, out HQ 0.0), match: 11.5  trail: 0.0  lead: -13.4  total: -2.2 
(0, 4) 21278-21286 [ 0.0] (0,29)   C ab090109r1         65-57 | 8 69 | LU: || local(+/-) (0.0,0.0), distant (0.0,0.0)
(0, 0) 20287-20292 [ 0.0] (978,992)   C ch070109r1         1049-1044 | 29 91 | LU:(**29 78**)(**88 91**) || local(+/-) (0.0,0.0), distant (0.0,0.0)
(0, 0) 22780-23726 [19.5] (27,0)   C da100109r1         1001-46 | (9 46)  46 1009 | DU:(**9 45**) [9 46  with   cd110109r1  110 147]  CHIMERIC || local(+/-) (20.4,0.0), distant (0.3,0.0)
(0, 0) 24538-25372 [12.6] (7,0)   C ba120109r1         905-66 | (1 62)  66 905 | DU:(**1 62**) [1 62  with   ac050109r1  98 162]  CHIMERIC || local(+/-) (15.8,0.0), distant (0.0,0.0)

Gaps in unique-read coverage:   I 1408- 2076

Subclone/read contig links and consistency checks (* = inconsistency; Contig 0 = singletons)
Max subclone size: 5000

Size histogram for consistent forward-reverse pairs (*** = inconsistent pairs)
  ***     0

 Consistent opp sense links (* = not used in chain, ** = multiple non-zero):