/data/tool/gcphrap aa.fasta.screen -ace -view -exp /data/ultra_disk/people/tomato/tomato_seq/C03HBa0001g02/workdir/all.assembly 
gcphrap version 0.990319

Run date:time  080911:114517
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    386 entries
Residue counts:
  A    70690
  C    43628
  G    53510
  N     3185
  T    66915
  X    150551
Total  388479

Read name analysis:
 # Reads      # templates
   1           386

 Suffix counts:
(no suffix) 386


Templates inferred from description field:     0
Templates inferred from name field:          386

Read-template multiplicity analysis:
 # Reads      # templates
   1           386

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

Chemistries inferred from name:
  386  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
  386  unknown (set to fwd)

Quality file: aa.fasta.screen.qual

Input quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56   95174  24.5   95174  24.5    0.24
 51   31825   8.2  126999  32.7    0.49
 50    4856   1.3  131855  33.9    0.54
 48    2147   0.6  134002  34.5    0.57
 47     841   0.2  134843  34.7    0.59
 46    3535   0.9  138378  35.6    0.68
 45    6262   1.6  144640  37.2    0.88
 44    4860   1.3  149500  38.5    1.07
 43    3389   0.9  152889  39.4    1.24
 42    9393   2.4  162282  41.8    1.83
 41     957   0.2  163239  42.0    1.91
 40   13948   3.6  177187  45.6    3.30
 39    1265   0.3  178452  45.9    3.46
 38     580   0.1  179032  46.1    3.56
 37    4442   1.1  183474  47.2    4.44
 36     587   0.2  184061  47.4    4.59
 35    4603   1.2  188664  48.6    6.05
 34    2296   0.6  190960  49.2    6.96
 33    3043   0.8  194003  49.9    8.48
 32    3044   0.8  197047  50.7   10.41
 31    1319   0.3  198366  51.1   11.45
 30    1630   0.4  199996  51.5   13.08
 29    5397   1.4  205393  52.9   19.88
 28    1637   0.4  207030  53.3   22.47
 27    2962   0.8  209992  54.1   28.38
 26    1215   0.3  211207  54.4   31.43
 25    3633   0.9  214840  55.3   42.92
 24    2954   0.8  217794  56.1   54.68
 23    2694   0.7  220488  56.8   68.18
 22    2293   0.6  222781  57.3   82.65
 21    3085   0.8  225866  58.1  107.16
 20    2967   0.8  228833  58.9  136.83
 19    4492   1.2  233325  60.1  193.38
 18    3151   0.8  236476  60.9  243.32
 17    3623   0.9  240099  61.8  315.61
 16    4315   1.1  244414  62.9  423.99
 15    4885   1.3  249299  64.2  578.47
 14    4679   1.2  253978  65.4  764.75
 13    7734   2.0  261712  67.4  1152.36
 12    7146   1.8  268858  69.2  1603.25
 11   12601   3.2  281459  72.5  2604.18
 10   15444   4.0  296903  76.4  4148.58
  9   30831   7.9  327734  84.4  8029.97
  8   23392   6.0  351126  90.4  11737.35
  7    9432   2.4  360558  92.8  13619.29
  6   16414   4.2  376972  97.0  17742.30
  4    8055   2.1  385027  99.1  20949.05
  0    3443   0.9  388470 100.0  24392.05
 -1       9   0.0  388479 100.0  24401.05   (quality -1 = terminal quality 0)

Avg. full length: 1006.4, trimmed (qual > -1): 1006.4
Avg. quality: 31.4 per base

Exact duplicate reads:  None.

Probable unremoved sequencing vector (matches excluded from assembly, quality reduced to 0): 
aa040109f1   20-27   TGCAGCCC
ac040109f1    9-28   AATCGANATTTCTGCAGCCC
ac050109f1    7-25   TGNTCGNNATNCTGCAGCC
ac090109f1   18-22   TCTGC
ae050109r1    6-48   CCCCCGGCGGTTGGCGGCCGCTCTAGAACTAGTGGGATCCCCC
ae100109r1   14-45   GGTGGCGGCCGCTCTAGACTAGTGGATCCCCC
af060109f1    6-22   TGATCGTAATTCTGCAG
af060109r1   44-46   CCC
af110109r1    9-48   CCCCGTCGGGTGGCGGCCGCTCTAGAACTAGTGGACCCCC
ag070109r1    5-47   CTCCCGCGGGTGGGGCGGCCGCTCTAGAACTAGTGGATCCCCC
ba010109r1    5-46   GGGCGGATTAGGGGCGGCCGCTCTAGAACTAGTGGATCCCCC
ba040109r1    6-46   CTCCCGCGGGGGGCGGCCGCTCTAGAACTAGTGGATCCCCC
bb090109r1    7-49   CCCCCGGCGGTTGGCGGCCGCTCTANGAACTAGTGGATCCCCC
bb100109r1    6-49   CCCCCGCCGGGTGGGCGGCCGCTCTAGAACTAGTGGGATCCCCC
bc010109r1   18-49   GGTGGCGGCCGCTCTAGACTAGTGGATCCCCC
bc040109f1    9-28   AATCGGAATNNCTGCAGCCC
bc060109r1    2-46   AGACTCCCGCCGGTGGCGGCCGCTCTANGAACTAGTGGATCCCCC
bc120109r1   21-51   GGGCGGCCGCTCTAGAACTAGTGGATCCCCC
bd100109r1   10-49   CCCCGTCTGGTGGCGGGCGCTCTAGAACTAGTGGACCCCC
be010109f1   20-26   TGCAGCC
be110109r1   16-47   GGTGGCGGCCGCTCTAGAACTAGTGGACCCCC
bf050109r1    2-46   AGACCCCCGCCGGTGGCGGCCGCTCTANGAACTAGTGGATCCCCC
bg070109r1    8-47   CCCGCCGGTGGCGGCCGCTCTAGAACTAGTGGGATCCCCC
bg090109f1   16-20   TCTGC
bg120109r1   14-47   GGTGGCGGCCGCTCTAGAACTAGTGGGATCCCCC
bh110109r1    9-51   GGGCGTATTAGNGGCGGCCGCTCTANGAACTAGTGGATCCCCC

Near duplicate reads: 
aa040109r1            bd010109f1      (imperfect: 47-956 (12)   46-947 (9) )
aa050109f1            bg080109f1      (imperfect: 33-978 (3)   26-961 (19) )
ac050109f1            af060109f1      (imperfect: 6-969 (4)   5-970 (14) )
ac090109f1            bg090109f1      (imperfect: 17-976 (11)   15-970 (7) )
ad100109r1            af120109r1      (imperfect: 49-932 (29)   49-929 (0) )
ad100109r1            ae040109f1      (imperfect: 49-958 (3)   45-955 (22) )
ae090109r1            bd020109f1      (imperfect: 48-966 (1)   42-973 (20) )
ah120109r1            bd020109r1      (imperfect: 47-937 (13)   48-936 (37) )

Internal read matches (same orientation) : 
 55   be120109f1    disjoint 69-mers  24-92 / 203-270 
 65   be120109r1    disjoint 68-mers  88-155 / 266-333 

No. of node-rejected pairs: None.

Multi-segment reads (initially rejected segments in parentheses) -- XXX means segments flank X'd region: 
ag020109f1          (30 80)  258 713 

1 reads with multiple segments.

Probable deletion reads (excluded from assembly): None.

Revised quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90   79707  20.5   79707  20.5    0.00
 89     137   0.0   79844  20.6    0.00
 88     199   0.1   80043  20.6    0.00
 87     253   0.1   80296  20.7    0.00
 86     129   0.0   80425  20.7    0.00
 85     287   0.1   80712  20.8    0.00
 84     244   0.1   80956  20.8    0.00
 83     241   0.1   81197  20.9    0.00
 82     169   0.0   81366  20.9    0.00
 81    1220   0.3   82586  21.3    0.00
 80      94   0.0   82680  21.3    0.00
 79     100   0.0   82780  21.3    0.00
 78      53   0.0   82833  21.3    0.00
 77     119   0.0   82952  21.4    0.00
 76     219   0.1   83171  21.4    0.00
 75     125   0.0   83296  21.4    0.00
 74      94   0.0   83390  21.5    0.00
 73      65   0.0   83455  21.5    0.00
 72      71   0.0   83526  21.5    0.00
 71     158   0.0   83684  21.5    0.00
 70     111   0.0   83795  21.6    0.00
 69     114   0.0   83909  21.6    0.00
 68      75   0.0   83984  21.6    0.00
 67     108   0.0   84092  21.6    0.00
 66    6403   1.6   90495  23.3    0.00
 65     297   0.1   90792  23.4    0.00
 64      78   0.0   90870  23.4    0.00
 63      81   0.0   90951  23.4    0.00
 62      83   0.0   91034  23.4    0.00
 61     534   0.1   91568  23.6    0.00
 60     311   0.1   91879  23.7    0.00
 59     138   0.0   92017  23.7    0.00
 58     115   0.0   92132  23.7    0.00
 57     162   0.0   92294  23.8    0.00
 56    9211   2.4  101505  26.1    0.03
 55     156   0.0  101661  26.2    0.03
 54     243   0.1  101904  26.2    0.03
 53     118   0.0  102022  26.3    0.03
 52     217   0.1  102239  26.3    0.03
 51    3297   0.8  105536  27.2    0.06
 50    1006   0.3  106542  27.4    0.07
 49     117   0.0  106659  27.5    0.07
 48     300   0.1  106959  27.5    0.07
 47     240   0.1  107199  27.6    0.08
 46     447   0.1  107646  27.7    0.09
 45     704   0.2  108350  27.9    0.11
 44     947   0.2  109297  28.1    0.15
 43     427   0.1  109724  28.2    0.17
 42    1366   0.4  111090  28.6    0.26
 41     315   0.1  111405  28.7    0.28
 40    3660   0.9  115065  29.6    0.65
 39     134   0.0  115199  29.7    0.66
 38     125   0.0  115324  29.7    0.68
 37     552   0.1  115876  29.8    0.79
 36     132   0.0  116008  29.9    0.83
 35     597   0.2  116605  30.0    1.02
 34     311   0.1  116916  30.1    1.14
 33     476   0.1  117392  30.2    1.38
 32     329   0.1  117721  30.3    1.59
 31     238   0.1  117959  30.4    1.77
 30     276   0.1  118235  30.4    2.05
 29     604   0.2  118839  30.6    2.81
 28     290   0.1  119129  30.7    3.27
 27     338   0.1  119467  30.8    3.95
 26     246   0.1  119713  30.8    4.56
 25     714   0.2  120427  31.0    6.82
 24     446   0.1  120873  31.1    8.60
 23     358   0.1  121231  31.2   10.39
 22     250   0.1  121481  31.3   11.97
 21     319   0.1  121800  31.4   14.50
 20     228   0.1  122028  31.4   16.78
 19     359   0.1  122387  31.5   21.30
 18     259   0.1  122646  31.6   25.41
 17     215   0.1  122861  31.6   29.70
 16     271   0.1  123132  31.7   36.50
 15     357   0.1  123489  31.8   47.79
 14     214   0.1  123703  31.8   56.31
 13     337   0.1  124040  31.9   73.20
 12     196   0.1  124236  32.0   85.57
 11     287   0.1  124523  32.1  108.37
 10     308   0.1  124831  32.1  139.17
  9     395   0.1  125226  32.2  188.89
  8     209   0.1  125435  32.3  222.02
  7     195   0.1  125630  32.3  260.93
  6      83   0.0  125713  32.4  281.77
  5      11   0.0  125724  32.4  285.25
  4      52   0.0  125776  32.4  305.95
  3       8   0.0  125784  32.4  309.96
  2   74439  19.2  200223  51.5  47277.80
  0    2684   0.7  202907  52.2  49961.80
 -1  185572  47.8  388479 100.0  235533.80   (quality -1 = terminal quality 0)

Avg. full length: 1006.4, trimmed (qual > -1): 525.7
Avg. quality: 24.7 per base

LLR score histogram:
Score    #   cum # 
-95.0     1     1
-60.0     1     2
-50.0     2     4
-25.0     2     6
-20.0    14    20
-10.0     2    22
 -5.0    15    37
  0.0   631   668
  5.0   614  1282
 10.0   512  1794
 15.0   388  2182
 20.0     8  2190

LLR score histogram:
Score    #   cum # 
-95.0     1     1
-80.0     2     3
-60.0     1     4
-25.0     2     6
-20.0    14    20
-10.0     2    22
 -5.0    15    37
  0.0   629   666
  5.0   615  1281
 10.0   512  1793
 15.0   389  2182
 20.0     8  2190

2d revised quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90   79569  20.5   79569  20.5    0.00
 89     139   0.0   79708  20.5    0.00
 88     205   0.1   79913  20.6    0.00
 87     255   0.1   80168  20.6    0.00
 86     137   0.0   80305  20.7    0.00
 85     294   0.1   80599  20.7    0.00
 84     251   0.1   80850  20.8    0.00
 83     241   0.1   81091  20.9    0.00
 82     169   0.0   81260  20.9    0.00
 81    1207   0.3   82467  21.2    0.00
 80      96   0.0   82563  21.3    0.00
 79     101   0.0   82664  21.3    0.00
 78      54   0.0   82718  21.3    0.00
 77     120   0.0   82838  21.3    0.00
 76     221   0.1   83059  21.4    0.00
 75     125   0.0   83184  21.4    0.00
 74      94   0.0   83278  21.4    0.00
 73      66   0.0   83344  21.5    0.00
 72      73   0.0   83417  21.5    0.00
 71     175   0.0   83592  21.5    0.00
 70     111   0.0   83703  21.5    0.00
 69     114   0.0   83817  21.6    0.00
 68      75   0.0   83892  21.6    0.00
 67     108   0.0   84000  21.6    0.00
 66    6362   1.6   90362  23.3    0.00
 65     296   0.1   90658  23.3    0.00
 64      78   0.0   90736  23.4    0.00
 63      81   0.0   90817  23.4    0.00
 62      83   0.0   90900  23.4    0.00
 61     530   0.1   91430  23.5    0.00
 60     311   0.1   91741  23.6    0.00
 59     138   0.0   91879  23.7    0.00
 58     115   0.0   91994  23.7    0.00
 57     162   0.0   92156  23.7    0.00
 56    9305   2.4  101461  26.1    0.03
 55     155   0.0  101616  26.2    0.03
 54     238   0.1  101854  26.2    0.03
 53     118   0.0  101972  26.2    0.03
 52     213   0.1  102185  26.3    0.03
 51    3320   0.9  105505  27.2    0.06
 50     994   0.3  106499  27.4    0.07
 49     109   0.0  106608  27.4    0.07
 48     300   0.1  106908  27.5    0.07
 47     236   0.1  107144  27.6    0.08
 46     456   0.1  107600  27.7    0.09
 45     706   0.2  108306  27.9    0.11
 44     951   0.2  109257  28.1    0.15
 43     428   0.1  109685  28.2    0.17
 42    1369   0.4  111054  28.6    0.26
 41     298   0.1  111352  28.7    0.28
 40    3678   0.9  115030  29.6    0.65
 39     137   0.0  115167  29.6    0.67
 38     125   0.0  115292  29.7    0.69
 37     554   0.1  115846  29.8    0.80
 36     133   0.0  115979  29.9    0.83
 35     605   0.2  116584  30.0    1.02
 34     310   0.1  116894  30.1    1.14
 33     478   0.1  117372  30.2    1.38
 32     330   0.1  117702  30.3    1.59
 31     238   0.1  117940  30.4    1.78
 30     274   0.1  118214  30.4    2.05
 29     606   0.2  118820  30.6    2.82
 28     298   0.1  119118  30.7    3.29
 27     342   0.1  119460  30.8    3.97
 26     248   0.1  119708  30.8    4.60
 25     711   0.2  120419  31.0    6.84
 24     444   0.1  120863  31.1    8.61
 23     358   0.1  121221  31.2   10.41
 22     250   0.1  121471  31.3   11.98
 21     320   0.1  121791  31.4   14.52
 20     240   0.1  122031  31.4   16.92
 19     359   0.1  122390  31.5   21.44
 18     259   0.1  122649  31.6   25.55
 17     219   0.1  122868  31.6   29.92
 16     271   0.1  123139  31.7   36.73
 15     361   0.1  123500  31.8   48.14
 14     214   0.1  123714  31.8   56.66
 13     336   0.1  124050  31.9   73.50
 12     199   0.1  124249  32.0   86.06
 11     289   0.1  124538  32.1  109.01
 10     315   0.1  124853  32.1  140.51
  9     403   0.1  125256  32.2  191.25
  8     215   0.1  125471  32.3  225.32
  7     271   0.1  125742  32.4  279.39
  6      95   0.0  125837  32.4  303.26
  5      60   0.0  125897  32.4  322.23
  4     108   0.0  126005  32.4  365.23
  3      57   0.0  126062  32.5  393.79
  2   74161  19.1  200223  51.5  47186.22
  0    2684   0.7  202907  52.2  49870.22
 -1  185572  47.8  388479 100.0  235442.22   (quality -1 = terminal quality 0)

Avg. full length: 1006.4, trimmed (qual > -1): 525.7
Avg. quality: 24.7 per base

No. confirmed reads: 150
Avg. length: 981.1, confirmed: 731.2, str. confirmed: 687.1, trimmed: 762.2
Preliminary clone size estimate: 9807 bp, depth of coverage: 11.2

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

25    54      54
24    34      88
23     1      89
22     8      97
21     7     104
20     1     105
19     2     107
18     1     108
13    10     118
12     4     122
11     1     123
 9     3     126
 8     1     127
 5     1     128
 3     2     130
 2     5     135
 1    15     150
 0   236     386

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: 
a0001g02t7_b03 80 819  left 
aa060109f1 29 135   right
aa090109f1 80 777  left right
aa090109r1 80 856  left right
ab030109f1 121 148  left right
ab030109r1 92 186  left right
ab070109r1 80 834  left 
ac100109r1 48 361   right
ad120109r1 80 843  left right
ag020109f1 287 318  left right
ag020109r1 46 736   right
ag030109f1 51 646  left 
ag030109r1 90 660  left 
ag080109f1 64 750  left 
ag080109r1 76 831  left 
ah070109f1 128 155   right
ah100109f1 131 511  left 
ah100109r1 135 562  left 
bb010109f1 80 785  left 
bb010109r1 43 654  left 
bd090109f1 43 649   right
bd120109r1 634 746  left 
be120109f1 33 312   right
be120109r1 46 349  left right
bf040109f1 80 817  left 
bf040109r1 80 876  left 
bg030109r1 48 263  left right

27 blocked reads: 13 left only, 6 right only, 8 both.
21 reads (not shown) lack a high-quality segment.

0 perfect duplicates

216 isolated singletons (having no non-vector match to any other read): 
  Read         Length      (# trimmed non-X bases)
 bc050109f1     974   (743)
 bc050109r1     981   (739)
 bc060109f1     985   (0)
 bc070109f1     974   (0)
 bc070109r1     978   (0)
 bc100109f1     974   (789)
 bc030109r1     973   (0)
 bb110109r1     986   (0)
 bb120109f1     964   (0)
 bb120109r1     945   (0)
 bc010109f1     995   (0)
 bc020109f1    1137   (0)
 bc030109f1     979   (0)
 bc100109r1     971   (789)
 bd060109r1    1006   (0)
 bd070109f1     977   (0)
 bd070109r1     985   (0)
 bd080109f1     985   (767)
 bd080109r1     994   (761)
 bd100109f1     985   (0)
 bd060109f1    1004   (0)
 bc110109f1    1000   (0)
 bc120109f1     955   (0)
 bd030109f1    1043   (0)
 bd030109r1    1030   (0)
 bd050109f1     982   (783)
 bd050109r1     993   (734)
 bb110109f1     969   (0)
 ba030109f1     972   (0)
 ba030109r1     979   (0)
 ba040109f1     977   (0)
 ba050109f1     986   (0)
 ba050109r1    1021   (0)
 ba080109f1    1153   (0)
 ba010109f1     964   (0)
 ah070109r1     999   (0)
 ah080109f1    1298   (0)
 ah080109r1    1250   (0)
 ah090109r1    1007   (0)
 ah110109f1    1294   (0)
 ah110109r1    1749   (0)
 ba080109r1     996   (0)
 bb020109r1     983   (0)
 bb040109f1    1000   (0)
 bb040109r1    1003   (0)
 bb050109f1     990   (0)
 bb050109r1    1000   (0)
 bb100109f1     971   (0)
 bb020109f1     972   (0)
 ba100109f1     966   (0)
 ba100109r1     973   (723)
 ba110109f1    1003   (0)
 ba110109r1    1027   (0)
 ba120109f1     948   (0)
 ba120109r1     944   (0)
 bd110109f1     960   (0)
 bf120109r1     947   (0)
 bg010109f1     941   (0)
 bg010109r1     942   (0)
 bg020109r1     967   (0)
 bg060109f1     982   (0)
 bg060109r1    1001   (0)
 bf120109f1     946   (0)
 bf080109f1     978   (0)
 bf080109r1     970   (0)
 bf090109f1    1099   (0)
 bf090109r1    1010   (0)
 bf110109f1     972   (0)
 bf110109r1     962   (0)
 bg110109f1    1057   (104)
 bh040109f1     969   (0)
 bh040109r1     973   (0)
 bh050109f1    1030   (0)
 bh050109r1    1029   (0)
 bh090109r1     971   (0)
 bh110109f1     961   (0)
 bh030109r1    1008   (0)
 bg110109r1     407   (0)
 bh010109f1     945   (0)
 bh010109r1    1042   (0)
 bh020109f1     956   (0)
 bh020109r1     943   (0)
 bh030109f1     976   (0)
 bf070109r1     979   (0)
 be050109f1     999   (684)
 be050109r1    1002   (703)
 be060109r1     987   (0)
 be070109f1     995   (605)
 be070109r1    1030   (439)
 be080109f1    1147   (218)
 be040109r1     981   (0)
 bd110109r1     953   (0)
 be020109f1     961   (0)
 be020109r1     953   (0)
 be030109f1     983   (768)
 be030109r1     982   (773)
 be040109f1    1002   (0)
 be080109r1     978   (741)
 bf030109f1     986   (0)
 bf030109r1     974   (0)
 bf050109f1     991   (0)
 bf060109f1    1082   (0)
 bf060109r1    1038   (0)
 bf070109f1     975   (0)
 bf020109r1     955   (0)
 be090109f1     978   (0)
 be090109r1    1530   (0)
 be100109f1     982   (0)
 be100109r1     974   (0)
 be110109f1     967   (0)
 bf010109r1     941   (0)
 bf020109f1     976   (0)
 ah090109f1    1074   (0)
 ac110109f1     966   (0)
 ac120109r1     950   (0)
 ad010109f1     989   (0)
 ad010109r1     966   (0)
 ad020109f1    1306   (0)
 ac080109r1     973   (0)
 ac030109r1     981   (725)
 ac060109f1     971   (0)
 ac060109r1     976   (0)
 ac070109f1     967   (0)
 ac070109r1     959   (0)
 ac080109f1     991   (0)
 ad020109r1    1358   (0)
 ad090109r1     962   (0)
 ad110109f1     949   (0)
 ad120109f1     969   (497)
 ae020109f1     946   (768)
 ae020109r1     950   (781)
 ae030109r1     972   (0)
 ad090109f1     961   (0)
 ad030109f1     983   (0)
 ad030109r1    1327   (0)
 ad040109f1     981   (752)
 ad040109r1    1007   (567)
 ad050109f1     972   (0)
 ad050109r1     972   (0)
 ac030109f1     977   (750)
 aa070109f1     966   (716)
 aa070109r1     962   (701)
 aa080109f1    1112   (0)
 aa080109r1    1357   (0)
 aa110109f1    1338   (0)
 aa110109r1    1017   (0)
 aa060109r1     970   (0)
 aa010109f1     963   (589)
 aa010109r1     962   (0)
 aa020109f1    1284   (0)
 aa020109r1    1188   (0)
 aa030109f1     986   (0)
 aa030109r1    1156   (0)
 aa120109f1    1373   (0)
 ab120109f1     934   (0)
 ab120109r1    1000   (0)
 ac010109f1     925   (0)
 ac010109r1    1002   (0)
 ac020109f1     978   (0)
 ac020109r1     959   (0)
 ab100109r1     953   (0)
 aa120109r1    1253   (0)
 ab010109r1    1093   (0)
 ab020109f1     984   (0)
 ab080109f1    1278   (0)
 ab080109r1    1861   (0)
 ab100109f1     951   (0)
 ad110109r1     964   (0)
 ag050109r1    1054   (84)
 ag060109f1     980   (0)
 ag060109r1     964   (0)
 ag070109f1    1009   (0)
 ag100109f1     990   (0)
 ag050109f1    1023   (260)
 af100109f1     959   (0)
 af100109r1    1740   (0)
 af110109f1     957   (0)
 ag010109r1     952   (0)
 ag040109f1     993   (578)
 ag040109r1    1011   (638)
 ag100109r1     969   (0)
 ah030109r1    1000   (0)
 ah040109f1    1056   (0)
 ah050109f1    1286   (0)
 ah050109r1    1116   (0)
 ah060109f1    1249   (0)
 ah060109r1    1610   (0)
 ah030109f1    1002   (0)
 ag120109f1    1030   (0)
 ag120109r1     956   (0)
 ah010109f1    1020   (0)
 ah010109r1     993   (78)
 ah020109f1     962   (0)
 ah020109r1    1424   (0)
 ag010109f1     949   (0)
 ae120109r1     938   (0)
 af010109f1     977   (0)
 af010109r1     979   (0)
 af020109r1     953   (0)
 af030109f1     986   (0)
 af030109r1     971   (0)
 ae120109f1     978   (0)
 ae050109f1    1002   (0)
 ae060109f1    1086   (0)
 ae060109r1    1016   (0)
 ae080109r1     963   (0)
 ae110109f1     954   (776)
 ae110109r1     947   (743)
 af080109r1     962   (0)
 af050109f1    1002   (0)
 af050109r1     984   (0)
 af080109f1    1011   (0)
 af070109r1    1028   (0)
 af070109f1    1068   (0)
 af040109r1    1074   (0)
 af040109f1    1225   (0)

Contig 1.  1 read; 939 bp (untrimmed), 764 (trimmed).
      1   939 ad120109r1    886 (  0)  0.00 0.00 0.00   46 (939)    0 (938) 

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56     456  48.6     456  48.6    0.00
 51     107  11.4     563  60.0    0.00
 48      10   1.1     573  61.0    0.00
 46       5   0.5     578  61.6    0.00
 45      42   4.5     620  66.0    0.00
 44       5   0.5     625  66.6    0.00
 43       3   0.3     628  66.9    0.00
 42       2   0.2     630  67.1    0.00
 40      46   4.9     676  72.0    0.01
 36       1   0.1     677  72.1    0.01
 34       4   0.4     681  72.5    0.01
 32      12   1.3     693  73.8    0.02
 31       1   0.1     694  73.9    0.02
 30       1   0.1     695  74.0    0.02
 29      21   2.2     716  76.3    0.05
 28       3   0.3     719  76.6    0.05
 27       1   0.1     720  76.7    0.05
 26       2   0.2     722  76.9    0.06
 25       8   0.9     730  77.7    0.08
 24       1   0.1     731  77.8    0.09
 23       1   0.1     732  78.0    0.09
 22       6   0.6     738  78.6    0.13
 21       3   0.3     741  78.9    0.15
 20       5   0.5     746  79.4    0.20
 18       3   0.3     749  79.8    0.25
 17       1   0.1     750  79.9    0.27
 16       2   0.2     752  80.1    0.32
 15       3   0.3     755  80.4    0.42
 14       1   0.1     756  80.5    0.46
 12       1   0.1     757  80.6    0.52
 11       3   0.3     760  80.9    0.76
 10       2   0.2     762  81.2    0.96
  9       2   0.2     764  81.4    1.21
 -1     175  18.6     939 100.0  176.21   (quality -1 = terminal quality 0)

Avg. full length: 939.0, trimmed (qual > -1): 764.0
Avg. quality: 40.5 per base

Initial, terminal qual 0 segments:  1-80, 845-939

Regions of LLR- adjusted quality < 2.0:
1-80, 812-817, 827-831, 834-837, 841-843, 845-939, 

6 regions, avg size 32.2, avg spacing 156.5

First_start: 939, 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)    47-  939 [17.0] (0,0)     ad120109r1         47-939 | 413 522 | DA:(**413 522**) || local(+/-) (0.0,0.0), distant (0.0,0.0)

Gaps in unique-read coverage:  None.

Contig 2.  2 reads; 216 bp (untrimmed), 216 (trimmed).  Isolated contig.
C  -700   264 bg030109r1    215 (  0)  0.00 0.00 0.00  701 (701)   48 ( 48) 
     -9   957 bg030109f1    196 (  0)  1.39 0.00 0.93   10 ( 10)  741 (741) 

Overall discrep rates (%):             0.69 0.00 0.46

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90     126  58.3     126  58.3    0.00
 89       3   1.4     129  59.7    0.00
 88       1   0.5     130  60.2    0.00
 87       4   1.9     134  62.0    0.00
 86       3   1.4     137  63.4    0.00
 85       9   4.2     146  67.6    0.00
 84       8   3.7     154  71.3    0.00
 83       3   1.4     157  72.7    0.00
 82       2   0.9     159  73.6    0.00
 81       4   1.9     163  75.5    0.00
 80       4   1.9     167  77.3    0.00
 79       3   1.4     170  78.7    0.00
 78       2   0.9     172  79.6    0.00
 77       1   0.5     173  80.1    0.00
 76       3   1.4     176  81.5    0.00
 75       1   0.5     177  81.9    0.00
 74       1   0.5     178  82.4    0.00
 73       1   0.5     179  82.9    0.00
 71       6   2.8     185  85.6    0.00
 66       2   0.9     187  86.6    0.00
 56      23  10.6     210  97.2    0.00
 51       6   2.8     216 100.0    0.00   (quality -1 = terminal quality 0)

Avg. full length: 216.0, trimmed (qual > -1): 216.0
Avg. quality: 82.7 per base

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

Regions of LLR- adjusted quality < 2.0:


1 regions, avg size 0.0, avg spacing 216.0

First_start: 1, last_end: 216

Slack, # used pairs (max_score), unused
 0     0  ( 0.0)     0 ( 0.0)        1
 1     1  ( 4.2)     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+
  217 - right        0+      bg030109f1   (  -9)    No            225+

Bottom strand: 
 left -     0        0+      bg030109r1   ( 264)    Yes           264+
  217 - 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    134    134    430 (100.00)     0  0    0   0   0   0     0 (0.00)    0    5 (1.16)
51     87    221    296 ( 68.84)     0  0    0   0   0   0     0 (0.00)    0    5 (1.69)
48      3    224    209 ( 48.60)     0  0    0   0   0   0     0 (0.00)    0    5 (2.39)
46     10    234    206 ( 47.91)     0  0    0   0   0   0     0 (0.00)    0    5 (2.43)
45     61    295    196 ( 45.58)     0  0    0   0   0   0     0 (0.00)    0    5 (2.55)
44      2    297    135 ( 31.40)     0  0    0   0   0   0     0 (0.00)    0    5 (3.70)
43      3    300    133 ( 30.93)     0  0    0   0   0   0     0 (0.00)    0    5 (3.76)
42     15    315    130 ( 30.23)     0  0    0   0   0   0     0 (0.00)    0    5 (3.85)
40     35    350    115 ( 26.74)     0  0    0   0   0   0     0 (0.00)    0    5 (4.35)
39      7    357     80 ( 18.60)     0  0    0   0   0   0     0 (0.00)    0    5 (6.25)
37      3    360     73 ( 16.98)     0  0    0   0   0   0     0 (0.00)    0    5 (6.85)
36      3    363     70 ( 16.28)     0  0    0   0   0   0     0 (0.00)    0    5 (7.14)
35      2    365     67 ( 15.58)     0  0    0   0   0   0     0 (0.00)    0    5 (7.46)
34      5    370     65 ( 15.12)     0  0    0   0   0   0     0 (0.00)    0    5 (7.69)
33      9    379     60 ( 13.95)     0  0    0   0   0   0     0 (0.00)    0    5 (8.33)
32      4    383     51 ( 11.86)     0  0    0   0   0   0     0 (0.00)    0    5 (9.80)
31      2    385     47 ( 10.93)     0  0    0   0   0   0     0 (0.00)    0    5 (10.64)
30      6    391     45 ( 10.47)     0  0    0   0   0   0     0 (0.00)    0    5 (11.11)
29      5    396     39 (  9.07)     0  0    0   0   0   0     0 (0.00)    0    5 (12.82)
28      1    397     34 (  7.91)     0  0    0   0   0   0     0 (0.00)    0    5 (14.71)
25      1    398     33 (  7.67)     0  0    0   0   0   0     0 (0.00)    0    5 (15.15)
24      1    399     32 (  7.44)     0  0    0   0   0   0     0 (0.00)    0    5 (15.62)
23      0    399     31 (  7.21)     0  0    0   0   0   0     0 (0.00)    0    5 (16.13)
22      3    402     31 (  7.21)     0  0    0   0   0   0     0 (0.00)    0    5 (16.13)
21      3    405     28 (  6.51)     0  0    0   0   0   0     0 (0.00)    0    5 (17.86)
20      0    405     25 (  5.81)     0  0    0   0   0   0     0 (0.00)    0    5 (20.00)
19      1    406     25 (  5.81)     0  0    0   0   0   0     0 (0.00)    0    5 (20.00)
18      1    407     24 (  5.58)     0  0    0   0   0   0     0 (0.00)    0    5 (20.83)
17      2    409     23 (  5.35)     0  0    0   0   0   1     1 (50.00)    1    5 (21.74)
16      2    411     21 (  4.88)     0  0    0   0   0   0     0 (0.00)    1    4 (19.05)
15      1    412     19 (  4.42)     0  0    0   0   0   0     0 (0.00)    1    4 (21.05)
14      1    413     18 (  4.19)     0  0    0   0   0   0     0 (0.00)    1    4 (22.22)
13      0    413     17 (  3.95)     0  0    0   0   0   0     0 (0.00)    1    4 (23.53)
12      1    414     17 (  3.95)     0  0    0   0   0   0     0 (0.00)    1    4 (23.53)
11      2    416     16 (  3.72)     0  0    0   0   0   0     0 (0.00)    1    4 (25.00)
10      4    420     14 (  3.26)     0  0    0   0   0   0     0 (0.00)    1    4 (28.57)
 9      7    427     10 (  2.33)     0  0    0   3   0   1     4 (57.14)    5    4 (40.00)
 8      3    430      3 (  0.70)     0  0    0   0   0   0     0 (0.00)    5    0 (0.00)
-1      0    430      0 (  0.00)     0  0    0   0   0   0     0 (0.00)    5    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    252    252    430 (100.00)     0  0    0   0   0   0     0 (0.00)    0    5 (1.16)
89      6    258    178 ( 41.40)     0  0    0   0   0   0     0 (0.00)    0    5 (2.81)
88      2    260    172 ( 40.00)     0  0    0   0   0   0     0 (0.00)    0    5 (2.91)
87      8    268    170 ( 39.53)     0  0    0   0   0   0     0 (0.00)    0    5 (2.94)
86      6    274    162 ( 37.67)     0  0    0   0   0   0     0 (0.00)    0    5 (3.09)
85     18    292    156 ( 36.28)     0  0    0   0   0   0     0 (0.00)    0    5 (3.21)
84     16    308    138 ( 32.09)     0  0    0   0   0   0     0 (0.00)    0    5 (3.62)
83      6    314    122 ( 28.37)     0  0    0   0   0   0     0 (0.00)    0    5 (4.10)
82      4    318    116 ( 26.98)     0  0    0   0   0   0     0 (0.00)    0    5 (4.31)
81      7    325    112 ( 26.05)     0  0    0   0   0   0     0 (0.00)    0    5 (4.46)
80      7    332    105 ( 24.42)     0  0    0   0   0   0     0 (0.00)    0    5 (4.76)
79      6    338     98 ( 22.79)     0  0    0   0   0   0     0 (0.00)    0    5 (5.10)
78      4    342     92 ( 21.40)     0  0    0   0   0   0     0 (0.00)    0    5 (5.43)
77      2    344     88 ( 20.47)     0  0    0   0   0   0     0 (0.00)    0    5 (5.68)
76      6    350     86 ( 20.00)     0  0    0   0   0   0     0 (0.00)    0    5 (5.81)
75      2    352     80 ( 18.60)     0  0    0   0   0   0     0 (0.00)    0    5 (6.25)
74      1    353     78 ( 18.14)     0  0    0   0   0   0     0 (0.00)    0    5 (6.41)
73      2    355     77 ( 17.91)     0  0    0   0   0   0     0 (0.00)    0    5 (6.49)
71      6    361     75 ( 17.44)     0  0    0   0   0   0     0 (0.00)    0    5 (6.67)
66      2    363     69 ( 16.05)     0  0    0   0   0   0     0 (0.00)    0    5 (7.25)
60      2    365     67 ( 15.58)     0  0    0   0   0   0     0 (0.00)    0    5 (7.46)
59      1    366     65 ( 15.12)     0  0    0   0   0   0     0 (0.00)    0    5 (7.69)
56     26    392     64 ( 14.88)     0  0    0   0   0   0     0 (0.00)    0    5 (7.81)
55      1    393     38 (  8.84)     0  0    0   0   0   0     0 (0.00)    0    5 (13.16)
51      7    400     37 (  8.60)     0  0    0   0   0   0     0 (0.00)    0    5 (13.51)
47      1    401     30 (  6.98)     0  0    0   0   0   0     0 (0.00)    0    5 (16.67)
46      1    402     29 (  6.74)     0  0    0   0   0   0     0 (0.00)    0    5 (17.24)
45      1    403     28 (  6.51)     0  0    0   0   0   0     0 (0.00)    0    5 (17.86)
36      1    404     27 (  6.28)     0  0    0   0   0   0     0 (0.00)    0    5 (18.52)
34      1    405     26 (  6.05)     0  0    0   0   0   0     0 (0.00)    0    5 (19.23)
32      1    406     25 (  5.81)     0  0    0   0   0   0     0 (0.00)    0    5 (20.00)
31      1    407     24 (  5.58)     0  0    0   0   0   0     0 (0.00)    0    5 (20.83)
30      1    408     23 (  5.35)     0  0    0   0   0   0     0 (0.00)    0    5 (21.74)
25      1    409     22 (  5.12)     0  0    0   0   0   0     0 (0.00)    0    5 (22.73)
21      2    411     21 (  4.88)     0  0    0   0   0   0     0 (0.00)    0    5 (23.81)
17      1    412     19 (  4.42)     0  0    0   0   0   1     1 (100.00)    1    5 (26.32)
16      1    413     18 (  4.19)     0  0    0   0   0   0     0 (0.00)    1    4 (22.22)
14      1    414     17 (  3.95)     0  0    0   0   0   0     0 (0.00)    1    4 (23.53)
12      1    415     16 (  3.72)     0  0    0   0   0   0     0 (0.00)    1    4 (25.00)
11      2    417     15 (  3.49)     0  0    0   0   0   0     0 (0.00)    1    4 (26.67)
10      3    420     13 (  3.02)     0  0    0   0   0   0     0 (0.00)    1    4 (30.77)
 9      7    427     10 (  2.33)     0  0    0   3   0   1     4 (57.14)    5    4 (40.00)
 8      3    430      3 (  0.70)     0  0    0   0   0   0     0 (0.00)    5    0 (0.00)
-1      0    430      0 (  0.00)     0  0    0   0   0   0     0 (0.00)    5    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
 51       6        6        1
 56      23       29        4
 66       2       31        4
 71       6       37        4
 73       1       38        5
 74       1       39        5
 75       1       40        6
 76       3       43        7
 77       1       44        7
 78       2       46        7
 79       3       49        7
 80       4       53        8
 81       4       57        8
 82       2       59        9
 83       3       62       10
 84       8       70       10
 85       9       79       10
 86       3       82        9
 87       4       86       10
 88       1       87       10
 89       3       90       10
 90     126      216        1

SS region: 0 (0.00%), 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):
  216     -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 3.  2 reads; 32 bp (untrimmed), 0 (trimmed).  Isolated contig.
    -16   980 bc010109r1     31 (  0)  0.00 0.00 0.00   17 ( 17)  948 (948) 
    -12   949 ae100109r1     31 (  0)  0.00 0.00 0.00   13 ( 13)  917 (917) 

Overall discrep rates (%):             0.00 0.00 0.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 -1      32 100.0      32 100.0   32.00   (quality -1 = terminal quality 0)

Avg. full length: 32.0, trimmed (qual > -1): 0.0
Avg. quality: 0.0 per base

Initial, terminal qual 0 segments:  1-32, (None)

Regions of LLR- adjusted quality < 2.0:
1-32, 

1 regions, avg size 32.0, avg spacing 32.0

First_start: 1, last_end: 32

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+
   33 - right        0+      ae100109r1   ( -12)    No             44+

Bottom strand: 
 left - right       32+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
51      2      2     64 (100.00)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
48      3      5     62 ( 96.88)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
46      2      7     59 ( 92.19)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
40      1      8     57 ( 89.06)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
37      1      9     56 ( 87.50)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
33      1     10     55 ( 85.94)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
32      3     13     54 ( 84.38)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
30      1     14     51 ( 79.69)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
29      4     18     50 ( 78.12)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
28      3     21     46 ( 71.88)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
27      1     22     43 ( 67.19)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
26      2     24     42 ( 65.62)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
24      1     25     40 ( 62.50)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
23      1     26     39 ( 60.94)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
22      2     28     38 ( 59.38)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
20      3     31     36 ( 56.25)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
19      2     33     33 ( 51.56)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
18      1     34     31 ( 48.44)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
17      1     35     30 ( 46.88)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
16      5     40     29 ( 45.31)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
15      5     45     24 ( 37.50)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
14      1     46     19 ( 29.69)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
13      4     50     18 ( 28.12)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
11      3     53     14 ( 21.88)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
10      2     55     11 ( 17.19)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
 9      4     59      9 ( 14.06)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
 7      4     63      5 (  7.81)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
 6      1     64      1 (  1.56)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)
-1      0     64      0 (  0.00)     0  0    0   0   0   0     0 (0.00)    0    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     64     64      0 (  0.00)     0  0    0   0   0   0     0 (0.00)    0    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      32       32        1

SS region: 32 (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): 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 4.  2 reads; 1418 bp (untrimmed), 1300 (trimmed).  Isolated contig.
      1   976 bf040109f1    939 (  0)  0.51 0.41 0.00    0 (518)    5 ( 20) 
C   489  1464 bf040109r1    875 (  0)  0.32 1.08 0.00    5 ( 34)   46 (507) 

Overall discrep rates (%):             0.42 0.74 0.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90      47   3.3      47   3.3    0.00
 89       1   0.1      48   3.4    0.00
 88       8   0.6      56   3.9    0.00
 87       5   0.4      61   4.3    0.00
 86       2   0.1      63   4.4    0.00
 85      13   0.9      76   5.4    0.00
 84       1   0.1      77   5.4    0.00
 83       7   0.5      84   5.9    0.00
 82       4   0.3      88   6.2    0.00
 81       9   0.6      97   6.8    0.00
 80      11   0.8     108   7.6    0.00
 79       2   0.1     110   7.8    0.00
 78       3   0.2     113   8.0    0.00
 77       9   0.6     122   8.6    0.00
 76      10   0.7     132   9.3    0.00
 75      14   1.0     146  10.3    0.00
 74       8   0.6     154  10.9    0.00
 73       7   0.5     161  11.4    0.00
 72      11   0.8     172  12.1    0.00
 71      20   1.4     192  13.5    0.00
 70      11   0.8     203  14.3    0.00
 69      19   1.3     222  15.7    0.00
 68       6   0.4     228  16.1    0.00
 67      14   1.0     242  17.1    0.00
 66      21   1.5     263  18.5    0.00
 65      14   1.0     277  19.5    0.00
 64      12   0.8     289  20.4    0.00
 63      11   0.8     300  21.2    0.00
 62       5   0.4     305  21.5    0.00
 61       6   0.4     311  21.9    0.00
 60       4   0.3     315  22.2    0.00
 59       8   0.6     323  22.8    0.00
 58       4   0.3     327  23.1    0.00
 56     623  43.9     950  67.0    0.00
 53       1   0.1     951  67.1    0.00
 52       1   0.1     952  67.1    0.00
 51     230  16.2    1182  83.4    0.00
 50       3   0.2    1185  83.6    0.00
 49       1   0.1    1186  83.6    0.00
 48       2   0.1    1188  83.8    0.00
 47       1   0.1    1189  83.9    0.00
 46       5   0.4    1194  84.2    0.00
 45      49   3.5    1243  87.7    0.01
 44       1   0.1    1244  87.7    0.01
 43       8   0.6    1252  88.3    0.01
 42       3   0.2    1255  88.5    0.01
 41       5   0.4    1260  88.9    0.01
 40      23   1.6    1283  90.5    0.01
 37       3   0.2    1286  90.7    0.01
 36       1   0.1    1287  90.8    0.01
 33       4   0.3    1291  91.0    0.01
 32       1   0.1    1292  91.1    0.01
 30       1   0.1    1293  91.2    0.01
 29       1   0.1    1294  91.3    0.01
 27       1   0.1    1295  91.3    0.02
 25       2   0.1    1297  91.5    0.02
 23       1   0.1    1298  91.5    0.03
 20       1   0.1    1299  91.6    0.04
 15       1   0.1    1300  91.7    0.07
 -1     118   8.3    1418 100.0  118.07   (quality -1 = terminal quality 0)

Avg. full length: 1418.0, trimmed (qual > -1): 1300.0
Avg. quality: 53.6 per base

Initial, terminal qual 0 segments:  1-84, 1385-1418

Regions of LLR- adjusted quality < 2.0:
1-84, 116, 1385-1418, 

3 regions, avg size 39.7, avg spacing 472.7

First_start: 519, last_end: 957

Slack, # used pairs (max_score), unused
 0     0  ( 0.0)     0 ( 0.0)        1
 3     1  (10.4)     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+
  972 - right      447+      bf040109f1   (   1)    No           1417+

Bottom strand: 
 left -   493      493+      bf040109r1   (1464)    No           1464+
 1419 - 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    790    790   1886 (100.00)     0  0    0   0   0   0     0 (0.00)    0   22 (1.17)
51    321   1111   1096 ( 58.11)     0  0    0   0   0   0     0 (0.00)    0   22 (2.01)
50      5   1116    775 ( 41.09)     0  0    0   0   0   0     0 (0.00)    0   22 (2.84)
48     18   1134    770 ( 40.83)     0  0    0   0   0   0     0 (0.00)    0   22 (2.86)
46     15   1149    752 ( 39.87)     0  0    0   0   0   0     0 (0.00)    0   22 (2.93)
45     73   1222    737 ( 39.08)     0  0    0   0   0   0     0 (0.00)    0   22 (2.99)
44      7   1229    664 ( 35.21)     0  0    0   0   0   0     0 (0.00)    0   22 (3.31)
43      8   1237    657 ( 34.84)     0  0    0   0   0   0     0 (0.00)    0   22 (3.35)
42     22   1259    649 ( 34.41)     0  0    0   0   0   0     0 (0.00)    0   22 (3.39)
41      5   1264    627 ( 33.24)     0  0    0   0   0   0     0 (0.00)    0   22 (3.51)
40     83   1347    622 ( 32.98)     0  0    0   0   0   0     0 (0.00)    0   22 (3.54)
39      5   1352    539 ( 28.58)     0  0    0   0   0   0     0 (0.00)    0   22 (4.08)
37     20   1372    534 ( 28.31)     0  0    0   0   0   0     0 (0.00)    0   22 (4.12)
36      1   1373    514 ( 27.25)     0  0    0   0   0   0     0 (0.00)    0   22 (4.28)
35      7   1380    513 ( 27.20)     0  0    0   0   0   0     0 (0.00)    0   22 (4.29)
34     14   1394    506 ( 26.83)     0  0    0   0   0   0     0 (0.00)    0   22 (4.35)
33      9   1403    492 ( 26.09)     0  0    0   0   0   0     0 (0.00)    0   22 (4.47)
32     30   1433    483 ( 25.61)     0  0    0   0   0   0     0 (0.00)    0   22 (4.55)
31      6   1439    453 ( 24.02)     0  0    0   0   0   0     0 (0.00)    0   22 (4.86)
30      4   1443    447 ( 23.70)     0  0    0   0   0   0     0 (0.00)    0   22 (4.92)
29     43   1486    443 ( 23.49)     0  0    0   0   0   0     0 (0.00)    0   22 (4.97)
28     10   1496    400 ( 21.21)     0  0    0   0   0   0     0 (0.00)    0   22 (5.50)
27     10   1506    390 ( 20.68)     0  0    0   0   0   0     0 (0.00)    0   22 (5.64)
26      2   1508    380 ( 20.15)     0  0    0   0   0   0     0 (0.00)    0   22 (5.79)
25     27   1535    378 ( 20.04)     0  0    0   0   0   0     0 (0.00)    0   22 (5.82)
24     12   1547    351 ( 18.61)     0  0    0   0   0   0     0 (0.00)    0   22 (6.27)
23      4   1551    339 ( 17.97)     0  0    0   0   0   0     0 (0.00)    0   22 (6.49)
22      4   1555    335 ( 17.76)     0  0    0   0   0   0     0 (0.00)    0   22 (6.57)
21      8   1563    331 ( 17.55)     0  0    0   0   0   0     0 (0.00)    0   22 (6.65)
20      8   1571    323 ( 17.13)     0  0    0   0   0   0     0 (0.00)    0   22 (6.81)
19     14   1585    315 ( 16.70)     0  0    0   0   0   0     0 (0.00)    0   22 (6.98)
18     11   1596    301 ( 15.96)     0  0    0   0   0   0     0 (0.00)    0   22 (7.31)
17     13   1609    290 ( 15.38)     0  0    0   0   0   0     0 (0.00)    0   22 (7.59)
16     13   1622    277 ( 14.69)     0  0    0   0   1   0     1 (7.69)    1   22 (7.94)
15     18   1640    264 ( 14.00)     0  0    0   0   0   0     0 (0.00)    1   21 (7.95)
14     19   1659    246 ( 13.04)     0  0    0   0   0   0     0 (0.00)    1   21 (8.54)
13     16   1675    227 ( 12.04)     0  0    0   0   0   0     0 (0.00)    1   21 (9.25)
12     24   1699    211 ( 11.19)     0  0    0   0   1   0     1 (4.17)    2   21 (9.95)
11     31   1730    187 (  9.92)     0  0    0   0   0   0     0 (0.00)    2   20 (10.70)
10     49   1779    156 (  8.27)     0  0    0   3   1   0     4 (8.16)    6   20 (12.82)
 9     40   1819    107 (  5.67)     0  0    0   0   4   0     4 (10.00)   10   16 (14.95)
 8     30   1849     67 (  3.55)     0  0    0   1   3   0     4 (13.33)   14   12 (17.91)
 7     33   1882     37 (  1.96)     0  0    0   4   4   0     8 (24.24)   22    8 (21.62)
 6      4   1886      4 (  0.21)     0  0    0   0   0   0     0 (0.00)   22    0 (0.00)
-1     24   1910      0 (  0.00)    10  0    0   0   0   0     0 (0.00)   22    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     94     94   1748 (100.00)     0  0    0   0   0   0     0 (0.00)    0   14 (0.80)
89      2     96   1654 ( 94.62)     0  0    0   0   0   0     0 (0.00)    0   14 (0.85)
88     16    112   1652 ( 94.51)     0  0    0   0   0   0     0 (0.00)    0   14 (0.85)
87     10    122   1636 ( 93.59)     0  0    0   0   0   0     0 (0.00)    0   14 (0.86)
86      4    126   1626 ( 93.02)     0  0    0   0   0   0     0 (0.00)    0   14 (0.86)
85     26    152   1622 ( 92.79)     0  0    0   0   0   0     0 (0.00)    0   14 (0.86)
84      1    153   1596 ( 91.30)     0  0    0   0   0   0     0 (0.00)    0   14 (0.88)
83     14    167   1595 ( 91.25)     0  0    0   0   0   0     0 (0.00)    0   14 (0.88)
82      8    175   1581 ( 90.45)     0  0    0   0   0   0     0 (0.00)    0   14 (0.89)
81     16    191   1573 ( 89.99)     0  0    0   0   0   0     0 (0.00)    0   14 (0.89)
80     22    213   1557 ( 89.07)     0  0    0   0   0   0     0 (0.00)    0   14 (0.90)
79      4    217   1535 ( 87.81)     0  0    0   0   0   0     0 (0.00)    0   14 (0.91)
78      6    223   1531 ( 87.59)     0  0    0   0   0   0     0 (0.00)    0   14 (0.91)
77     16    239   1525 ( 87.24)     0  0    0   0   0   0     0 (0.00)    0   14 (0.92)
76     19    258   1509 ( 86.33)     0  0    0   0   0   0     0 (0.00)    0   14 (0.93)
75     25    283   1490 ( 85.24)     0  0    0   0   0   0     0 (0.00)    0   14 (0.94)
74     12    295   1465 ( 83.81)     0  0    0   0   0   0     0 (0.00)    0   14 (0.96)
73     10    305   1453 ( 83.12)     0  0    0   0   0   0     0 (0.00)    0   14 (0.96)
72     20    325   1443 ( 82.55)     0  0    0   0   0   0     0 (0.00)    0   14 (0.97)
71     23    348   1423 ( 81.41)     0  0    0   0   0   0     0 (0.00)    0   14 (0.98)
70     22    370   1400 ( 80.09)     0  0    0   0   0   0     0 (0.00)    0   14 (1.00)
69     30    400   1378 ( 78.83)     0  0    0   0   0   0     0 (0.00)    0   14 (1.02)
68      6    406   1348 ( 77.12)     0  0    0   0   0   0     0 (0.00)    0   14 (1.04)
67     18    424   1342 ( 76.77)     0  0    0   0   0   0     0 (0.00)    0   14 (1.04)
66     29    453   1324 ( 75.74)     0  0    0   0   0   0     0 (0.00)    0   14 (1.06)
65     22    475   1295 ( 74.08)     0  0    0   0   0   0     0 (0.00)    0   14 (1.08)
64     16    491   1273 ( 72.83)     0  0    0   0   0   0     0 (0.00)    0   14 (1.10)
63     13    504   1257 ( 71.91)     0  0    0   0   0   0     0 (0.00)    0   14 (1.11)
62      9    513   1244 ( 71.17)     0  0    0   0   0   0     0 (0.00)    0   14 (1.13)
61      9    522   1235 ( 70.65)     0  0    0   0   0   0     0 (0.00)    0   14 (1.13)
60      4    526   1226 ( 70.14)     0  0    0   0   0   0     0 (0.00)    0   14 (1.14)
59     14    540   1222 ( 69.91)     0  0    0   0   0   0     0 (0.00)    0   14 (1.15)
58      7    547   1208 ( 69.11)     0  0    0   0   0   0     0 (0.00)    0   14 (1.16)
57      1    548   1201 ( 68.71)     0  0    0   0   0   0     0 (0.00)    0   14 (1.17)
56    688   1236   1200 ( 68.65)     0  0    0   0   0   0     0 (0.00)    0   14 (1.17)
55      1   1237    512 ( 29.29)     0  0    0   0   0   0     0 (0.00)    0   14 (2.73)
53      2   1239    511 ( 29.23)     0  0    0   0   0   0     0 (0.00)    0   14 (2.74)
52      2   1241    509 ( 29.12)     0  0    0   0   0   0     0 (0.00)    0   14 (2.75)
51    263   1504    507 ( 29.00)     0  0    0   0   0   0     0 (0.00)    0   14 (2.76)
50      5   1509    244 ( 13.96)     0  0    0   0   0   0     0 (0.00)    0   14 (5.74)
49      1   1510    239 ( 13.67)     0  0    0   0   0   0     0 (0.00)    0   14 (5.86)
48      3   1513    238 ( 13.62)     0  0    0   0   0   0     0 (0.00)    0   14 (5.88)
47      1   1514    235 ( 13.44)     0  0    0   0   0   0     0 (0.00)    0   14 (5.96)
46      5   1519    234 ( 13.39)     0  0    0   0   0   0     0 (0.00)    0   14 (5.98)
45     52   1571    229 ( 13.10)     0  0    0   0   0   0     0 (0.00)    0   14 (6.11)
44      1   1572    177 ( 10.13)     0  0    0   0   0   0     0 (0.00)    0   14 (7.91)
43     10   1582    176 ( 10.07)     0  0    0   0   0   0     0 (0.00)    0   14 (7.95)
42      4   1586    166 (  9.50)     0  0    0   0   0   0     0 (0.00)    0   14 (8.43)
41      6   1592    162 (  9.27)     0  0    0   0   0   0     0 (0.00)    0   14 (8.64)
40     24   1616    156 (  8.92)     0  0    0   0   0   0     0 (0.00)    0   14 (8.97)
37      3   1619    132 (  7.55)     0  0    0   0   0   0     0 (0.00)    0   14 (10.61)
36      1   1620    129 (  7.38)     0  0    0   0   0   0     0 (0.00)    0   14 (10.85)
33      5   1625    128 (  7.32)     0  0    0   0   0   0     0 (0.00)    0   14 (10.94)
32      3   1628    123 (  7.04)     0  0    0   0   0   0     0 (0.00)    0   14 (11.38)
30      1   1629    120 (  6.86)     0  0    0   0   0   0     0 (0.00)    0   14 (11.67)
29      3   1632    119 (  6.81)     0  0    0   0   0   0     0 (0.00)    0   14 (11.76)
28      1   1633    116 (  6.64)     0  0    0   0   0   0     0 (0.00)    0   14 (12.07)
27      5   1638    115 (  6.58)     0  0    0   0   0   0     0 (0.00)    0   14 (12.17)
26      5   1643    110 (  6.29)     0  0    0   0   0   0     0 (0.00)    0   14 (12.73)
25      9   1652    105 (  6.01)     0  0    0   0   0   0     0 (0.00)    0   14 (13.33)
24      5   1657     96 (  5.49)     0  0    0   0   0   0     0 (0.00)    0   14 (14.58)
23      4   1661     91 (  5.21)     0  0    0   0   0   0     0 (0.00)    0   14 (15.38)
22      1   1662     87 (  4.98)     0  0    0   0   0   0     0 (0.00)    0   14 (16.09)
20      1   1663     86 (  4.92)     0  0    0   0   0   0     0 (0.00)    0   14 (16.28)
19      1   1664     85 (  4.86)     0  0    0   0   0   0     0 (0.00)    0   14 (16.47)
18      1   1665     84 (  4.81)     0  0    0   0   0   0     0 (0.00)    0   14 (16.67)
17      2   1667     83 (  4.75)     0  0    0   0   0   0     0 (0.00)    0   14 (16.87)
16      2   1669     81 (  4.63)     0  0    0   0   1   0     1 (50.00)    1   14 (17.28)
15      6   1675     79 (  4.52)     0  0    0   0   0   0     0 (0.00)    1   13 (16.46)
13      2   1677     73 (  4.18)     0  0    0   0   0   0     0 (0.00)    1   13 (17.81)
12      9   1686     71 (  4.06)     0  0    0   0   1   0     1 (11.11)    2   13 (18.31)
11     11   1697     62 (  3.55)     0  0    0   0   0   0     0 (0.00)    2   12 (19.35)
10     15   1712     51 (  2.92)     0  0    0   2   1   0     3 (20.00)    5   12 (23.53)
 9     10   1722     36 (  2.06)     0  0    0   0   3   0     3 (30.00)    8    9 (25.00)
 8      6   1728     26 (  1.49)     0  0    0   0   2   0     2 (33.33)   10    6 (23.08)
 7     19   1747     20 (  1.14)     0  0    0   2   2   0     4 (21.05)   14    4 (20.00)
 6      1   1748      1 (  0.06)     0  0    0   0   0   0     0 (0.00)   14    0 (0.00)
-1    162   1910      0 (  0.00)    10  0    0   4   4   0     8 (4.94)   22    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     118      118        2
 15       1      119        3
 20       1      120        3
 23       1      121        3
 25       2      123        3
 27       1      124        3
 29       1      125        3
 30       1      126        4
 32       1      127        3
 33       4      131        3
 36       1      132        3
 37       3      135        4
 40      23      158        9
 41       5      163       10
 42       3      166       12
 43       8      174       12
 44       1      175       13
 45      49      224       22
 46       5      229       22
 47       1      230       23
 48       2      232       23
 49       1      233       23
 50       3      236       23
 51     230      466       44
 52       1      467       44
 53       1      468       43
 56     623     1091        5
 58       4     1095        8
 59       8     1103       13
 60       4     1107       14
 61       6     1113       15
 62       5     1118       16
 63      11     1129       18
 64      12     1141       20
 65      14     1155       22
 66      21     1176       26
 67      14     1190       26
 68       6     1196       24
 69      19     1215       27
 70      11     1226       27
 71      20     1246       28
 72      11     1257       27
 73       7     1264       26
 74       8     1272       25
 75      14     1286       24
 76      10     1296       23
 77       9     1305       22
 78       3     1308       21
 79       2     1310       20
 80      11     1321       22
 81       9     1330       22
 82       4     1334       23
 83       7     1341       22
 84       1     1342       21
 85      13     1355       16
 86       2     1357       17
 87       5     1362       17
 88       8     1370       15
 89       1     1371       14
 90      47     1418        1

SS region: 940 (66.29%), 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): 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 5.  2 reads; 990 bp (untrimmed), 498 (trimmed).  Isolated contig.
C  -279   700 ah100109r1    530 (  0)  2.99 0.50 0.17  280 (391)   98 (133) 
    -14   990 ah100109f1    887 (  0)  2.22 0.30 0.10   15 (127)    0 (420) 

Overall discrep rates (%):             2.51 0.38 0.13

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 86       1   0.1       1   0.1    0.00
 83       5   0.5       6   0.6    0.00
 81       4   0.4      10   1.0    0.00
 80       2   0.2      12   1.2    0.00
 79       9   0.9      21   2.1    0.00
 77       3   0.3      24   2.4    0.00
 76       3   0.3      27   2.7    0.00
 75       9   0.9      36   3.6    0.00
 74       8   0.8      44   4.4    0.00
 72      11   1.1      55   5.6    0.00
 71       7   0.7      62   6.3    0.00
 70      14   1.4      76   7.7    0.00
 68       8   0.8      84   8.5    0.00
 67      15   1.5      99  10.0    0.00
 66      14   1.4     113  11.4    0.00
 65       9   0.9     122  12.3    0.00
 64       5   0.5     127  12.8    0.00
 63      14   1.4     141  14.2    0.00
 62       8   0.8     149  15.1    0.00
 61      11   1.1     160  16.2    0.00
 60      14   1.4     174  17.6    0.00
 59      22   2.2     196  19.8    0.00
 58      10   1.0     206  20.8    0.00
 57      17   1.7     223  22.5    0.00
 56      19   1.9     242  24.4    0.00
 55       9   0.9     251  25.4    0.00
 54      12   1.2     263  26.6    0.00
 53       5   0.5     268  27.1    0.00
 52      11   1.1     279  28.2    0.00
 51       6   0.6     285  28.8    0.00
 50      19   1.9     304  30.7    0.00
 49       3   0.3     307  31.0    0.00
 48      14   1.4     321  32.4    0.00
 47       5   0.5     326  32.9    0.00
 46       4   0.4     330  33.3    0.00
 45       4   0.4     334  33.7    0.00
 44      18   1.8     352  35.6    0.00
 43       9   0.9     361  36.5    0.00
 42      29   2.9     390  39.4    0.00
 41       3   0.3     393  39.7    0.00
 40       2   0.2     395  39.9    0.00
 39       4   0.4     399  40.3    0.01
 38       7   0.7     406  41.0    0.01
 37       5   0.5     411  41.5    0.01
 36       3   0.3     414  41.8    0.01
 35       4   0.4     418  42.2    0.01
 34       5   0.5     423  42.7    0.01
 33      11   1.1     434  43.8    0.02
 32       2   0.2     436  44.0    0.02
 31       1   0.1     437  44.1    0.02
 30       1   0.1     438  44.2    0.02
 29       6   0.6     444  44.8    0.03
 27       7   0.7     451  45.6    0.04
 26       2   0.2     453  45.8    0.05
 24       2   0.2     455  46.0    0.05
 23       8   0.8     463  46.8    0.09
 21       1   0.1     464  46.9    0.10
 19       4   0.4     468  47.3    0.15
 18       1   0.1     469  47.4    0.17
 17       8   0.8     477  48.2    0.33
 16       6   0.6     483  48.8    0.48
 15       4   0.4     487  49.2    0.61
 14       2   0.2     489  49.4    0.68
 12       4   0.4     493  49.8    0.94
 11       2   0.2     495  50.0    1.10
  9       3   0.3     498  50.3    1.47
 -1     492  49.7     990 100.0  493.47   (quality -1 = terminal quality 0)

Avg. full length: 990.0, trimmed (qual > -1): 498.0
Avg. quality: 26.1 per base

Initial, terminal qual 0 segments:  1-101, 600-990

Regions of LLR- adjusted quality < 2.0:
1-104, 108-116, 158-160, 570-575, 580-589, 597-990, 

6 regions, avg size 87.7, avg spacing 165.0

First_start: 112, last_end: 570

Slack, # used pairs (max_score), unused
 0     0  ( 0.0)     0 ( 0.0)        1
 2     1  ( 9.3)     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+
  991 - right        0+      ah100109f1   ( -14)    No           1004+

Bottom strand: 
 left -     0        0+      ah100109r1   ( 700)    Yes           700+
  603 - right      388+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56      4      4   1208 (100.00)     0  0    0   0   0   0     0 (0.00)    0   48 (3.97)
50     20     24   1204 ( 99.67)     0  0    0   0   0   0     0 (0.00)    0   48 (3.99)
48      2     26   1184 ( 98.01)     0  0    0   0   0   0     0 (0.00)    0   48 (4.05)
47      3     29   1182 ( 97.85)     0  0    0   0   0   0     0 (0.00)    0   48 (4.06)
46      3     32   1179 ( 97.60)     0  0    0   0   0   0     0 (0.00)    0   48 (4.07)
44     59     91   1176 ( 97.35)     0  0    0   0   0   0     0 (0.00)    0   48 (4.08)
43      1     92   1117 ( 92.47)     0  0    0   0   0   0     0 (0.00)    0   48 (4.30)
42     75    167   1116 ( 92.38)     0  0    0   0   0   0     0 (0.00)    0   48 (4.30)
41     11    178   1041 ( 86.18)     0  0    0   0   0   0     0 (0.00)    0   48 (4.61)
40     14    192   1030 ( 85.26)     0  0    0   0   0   0     0 (0.00)    0   48 (4.66)
39      8    200   1016 ( 84.11)     0  0    0   0   0   0     0 (0.00)    0   48 (4.72)
38      3    203   1008 ( 83.44)     0  0    0   0   0   0     0 (0.00)    0   48 (4.76)
37     54    257   1005 ( 83.20)     0  0    0   0   0   0     0 (0.00)    0   48 (4.78)
36      3    260    951 ( 78.73)     0  0    0   0   0   0     0 (0.00)    0   48 (5.05)
35     62    322    948 ( 78.48)     0  0    0   0   0   0     0 (0.00)    0   48 (5.06)
34     13    335    886 ( 73.34)     0  0    0   0   0   0     0 (0.00)    0   48 (5.42)
33    101    436    873 ( 72.27)     0  0    0   0   0   0     0 (0.00)    0   48 (5.50)
32     13    449    772 ( 63.91)     0  0    0   0   0   0     0 (0.00)    0   48 (6.22)
31     20    469    759 ( 62.83)     0  0    0   0   0   0     0 (0.00)    0   48 (6.32)
30     32    501    739 ( 61.18)     0  0    0   0   0   0     0 (0.00)    0   48 (6.50)
29     50    551    707 ( 58.53)     0  0    0   0   0   0     0 (0.00)    0   48 (6.79)
28     22    573    657 ( 54.39)     0  0    0   0   0   0     0 (0.00)    0   48 (7.31)
27     27    600    635 ( 52.57)     0  0    0   1   0   0     1 (3.70)    1   48 (7.56)
26     17    617    608 ( 50.33)     0  0    0   2   0   0     2 (11.76)    3   47 (7.73)
25     15    632    591 ( 48.92)     0  0    0   0   0   0     0 (0.00)    3   45 (7.61)
24     29    661    576 ( 47.68)     0  0    0   0   0   0     0 (0.00)    3   45 (7.81)
23     46    707    547 ( 45.28)     0  0    0   0   1   0     1 (2.17)    4   45 (8.23)
22     22    729    501 ( 41.47)     0  0    0   1   1   0     2 (9.09)    6   44 (8.78)
21     46    775    479 ( 39.65)     0  0    0   4   0   0     4 (8.70)   10   42 (8.77)
20     12    787    433 ( 35.84)     0  0    0   0   0   0     0 (0.00)   10   38 (8.78)
19     31    818    421 ( 34.85)     0  0    0   2   0   0     2 (6.45)   12   38 (9.03)
18     17    835    390 ( 32.28)     0  0    0   2   0   1     3 (17.65)   15   36 (9.23)
17     23    858    373 ( 30.88)     0  0    0   0   0   0     0 (0.00)   15   33 (8.85)
16     26    884    350 ( 28.97)     0  0    0   3   1   0     4 (15.38)   19   33 (9.43)
15     25    909    324 ( 26.82)     0  0    0   0   0   0     0 (0.00)   19   29 (8.95)
14     12    921    299 ( 24.75)     0  0    0   0   0   0     0 (0.00)   19   29 (9.70)
13     36    957    287 ( 23.76)     0  0    0   1   0   0     1 (2.78)   20   29 (10.10)
12     29    986    251 ( 20.78)     0  0    0   0   0   0     0 (0.00)   20   28 (11.16)
11     61   1047    222 ( 18.38)     0  0    0   5   0   0     5 (8.20)   25   28 (12.61)
10     35   1082    161 ( 13.33)     0  0    0   1   0   1     2 (5.71)   27   23 (14.29)
 9     79   1161    126 ( 10.43)     0  0    0   9   0   0     9 (11.39)   36   21 (16.67)
 8     23   1184     47 (  3.89)     0  0    0   3   0   0     3 (13.04)   39   12 (25.53)
 7     11   1195     24 (  1.99)     0  0    0   3   2   0     5 (45.45)   44    9 (37.50)
 6     11   1206     13 (  1.08)     0  0    0   3   0   0     3 (27.27)   47    4 (30.77)
 4      2   1208      2 (  0.17)     0  0    0   0   1   0     1 (50.00)   48    1 (50.00)
-1    388   1596      0 (  0.00)    98  0    0   0   0   0     0 (0.00)   48    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 (%)
86      2      2    958 (100.00)     0  0    0   0   0   0     0 (0.00)    0   13 (1.36)
83     10     12    956 ( 99.79)     0  0    0   0   0   0     0 (0.00)    0   13 (1.36)
81      8     20    946 ( 98.75)     0  0    0   0   0   0     0 (0.00)    0   13 (1.37)
80      4     24    938 ( 97.91)     0  0    0   0   0   0     0 (0.00)    0   13 (1.39)
79     18     42    934 ( 97.49)     0  0    0   0   0   0     0 (0.00)    0   13 (1.39)
77      6     48    916 ( 95.62)     0  0    0   0   0   0     0 (0.00)    0   13 (1.42)
76      6     54    910 ( 94.99)     0  0    0   0   0   0     0 (0.00)    0   13 (1.43)
75     17     71    904 ( 94.36)     0  0    0   0   0   0     0 (0.00)    0   13 (1.44)
74     16     87    887 ( 92.59)     0  0    0   0   0   0     0 (0.00)    0   13 (1.47)
72     20    107    871 ( 90.92)     0  0    0   0   0   0     0 (0.00)    0   13 (1.49)
71     13    120    851 ( 88.83)     0  0    0   0   0   0     0 (0.00)    0   13 (1.53)
70     28    148    838 ( 87.47)     0  0    0   0   0   0     0 (0.00)    0   13 (1.55)
69      1    149    810 ( 84.55)     0  0    0   0   0   0     0 (0.00)    0   13 (1.60)
68     16    165    809 ( 84.45)     0  0    0   0   0   0     0 (0.00)    0   13 (1.61)
67     25    190    793 ( 82.78)     0  0    0   0   0   0     0 (0.00)    0   13 (1.64)
66     28    218    768 ( 80.17)     0  0    0   0   0   0     0 (0.00)    0   13 (1.69)
65     15    233    740 ( 77.24)     0  0    0   0   0   0     0 (0.00)    0   13 (1.76)
64      8    241    725 ( 75.68)     0  0    0   0   0   0     0 (0.00)    0   13 (1.79)
63     26    267    717 ( 74.84)     0  0    0   0   0   0     0 (0.00)    0   13 (1.81)
62     15    282    691 ( 72.13)     0  0    0   0   0   0     0 (0.00)    0   13 (1.88)
61     22    304    676 ( 70.56)     0  0    0   0   0   0     0 (0.00)    0   13 (1.92)
60     25    329    654 ( 68.27)     0  0    0   0   0   0     0 (0.00)    0   13 (1.99)
59     29    358    629 ( 65.66)     0  0    0   0   0   0     0 (0.00)    0   13 (2.07)
58     19    377    600 ( 62.63)     0  0    0   0   0   0     0 (0.00)    0   13 (2.17)
57     24    401    581 ( 60.65)     0  0    0   0   0   0     0 (0.00)    0   13 (2.24)
56     34    435    557 ( 58.14)     0  0    0   0   0   0     0 (0.00)    0   13 (2.33)
55     15    450    523 ( 54.59)     0  0    0   0   0   0     0 (0.00)    0   13 (2.49)
54     22    472    508 ( 53.03)     0  0    0   0   0   0     0 (0.00)    0   13 (2.56)
53     16    488    486 ( 50.73)     0  0    0   0   0   0     0 (0.00)    0   13 (2.67)
52     16    504    470 ( 49.06)     0  0    0   0   0   0     0 (0.00)    0   13 (2.77)
51     10    514    454 ( 47.39)     0  0    0   0   0   0     0 (0.00)    0   13 (2.86)
50     26    540    444 ( 46.35)     0  0    0   0   0   0     0 (0.00)    0   13 (2.93)
49      5    545    418 ( 43.63)     0  0    0   0   0   0     0 (0.00)    0   13 (3.11)
48     20    565    413 ( 43.11)     0  0    0   0   0   0     0 (0.00)    0   13 (3.15)
47     10    575    393 ( 41.02)     0  0    0   0   0   0     0 (0.00)    0   13 (3.31)
46     10    585    383 ( 39.98)     0  0    0   0   0   0     0 (0.00)    0   13 (3.39)
45     10    595    373 ( 38.94)     0  0    0   0   0   0     0 (0.00)    0   13 (3.49)
44     27    622    363 ( 37.89)     0  0    0   0   0   0     0 (0.00)    0   13 (3.58)
43     16    638    336 ( 35.07)     0  0    0   0   0   0     0 (0.00)    0   13 (3.87)
42     41    679    320 ( 33.40)     0  0    0   0   0   0     0 (0.00)    0   13 (4.06)
41      4    683    279 ( 29.12)     0  0    0   0   0   0     0 (0.00)    0   13 (4.66)
40      4    687    275 ( 28.71)     0  0    0   0   0   0     0 (0.00)    0   13 (4.73)
39      7    694    271 ( 28.29)     0  0    0   0   0   0     0 (0.00)    0   13 (4.80)
38     10    704    264 ( 27.56)     0  0    0   0   0   0     0 (0.00)    0   13 (4.92)
37     11    715    254 ( 26.51)     0  0    0   0   0   0     0 (0.00)    0   13 (5.12)
36      8    723    243 ( 25.37)     0  0    0   0   0   0     0 (0.00)    0   13 (5.35)
35     10    733    235 ( 24.53)     0  0    0   0   0   0     0 (0.00)    0   13 (5.53)
34     12    745    225 ( 23.49)     0  0    0   0   0   0     0 (0.00)    0   13 (5.78)
33     20    765    213 ( 22.23)     0  0    0   0   0   0     0 (0.00)    0   13 (6.10)
32      7    772    193 ( 20.15)     0  0    0   0   0   0     0 (0.00)    0   13 (6.74)
31      5    777    186 ( 19.42)     0  0    0   0   0   0     0 (0.00)    0   13 (6.99)
30     15    792    181 ( 18.89)     0  0    0   0   0   0     0 (0.00)    0   13 (7.18)
29     13    805    166 ( 17.33)     0  0    0   0   0   0     0 (0.00)    0   13 (7.83)
28      8    813    153 ( 15.97)     0  0    0   0   0   0     0 (0.00)    0   13 (8.50)
27     11    824    145 ( 15.14)     0  0    0   0   0   0     0 (0.00)    0   13 (8.97)
26     11    835    134 ( 13.99)     0  0    0   0   0   0     0 (0.00)    0   13 (9.70)
25      3    838    123 ( 12.84)     0  0    0   0   0   0     0 (0.00)    0   13 (10.57)
24      8    846    120 ( 12.53)     0  0    0   0   0   0     0 (0.00)    0   13 (10.83)
23     15    861    112 ( 11.69)     0  0    0   0   1   0     1 (6.67)    1   13 (11.61)
22      2    863     97 ( 10.13)     0  0    0   0   1   0     1 (50.00)    2   12 (12.37)
21      2    865     95 (  9.92)     0  0    0   1   0   0     1 (50.00)    3   11 (11.58)
19      7    872     93 (  9.71)     0  0    0   0   0   0     0 (0.00)    3   10 (10.75)
18      1    873     86 (  8.98)     0  0    0   0   0   0     0 (0.00)    3   10 (11.63)
17      8    881     85 (  8.87)     0  0    0   0   0   0     0 (0.00)    3   10 (11.76)
16      7    888     77 (  8.04)     0  0    0   0   0   0     0 (0.00)    3   10 (12.99)
15      8    896     70 (  7.31)     0  0    0   0   0   0     0 (0.00)    3   10 (14.29)
14      2    898     62 (  6.47)     0  0    0   0   0   0     0 (0.00)    3   10 (16.13)
13      7    905     60 (  6.26)     0  0    0   1   0   0     1 (14.29)    4   10 (16.67)
12      4    909     53 (  5.53)     0  0    0   0   0   0     0 (0.00)    4    9 (16.98)
11     13    922     49 (  5.11)     0  0    0   3   0   0     3 (23.08)    7    9 (18.37)
10      9    931     36 (  3.76)     0  0    0   0   0   0     0 (0.00)    7    6 (16.67)
 9     20    951     27 (  2.82)     0  0    0   4   0   0     4 (20.00)   11    6 (22.22)
 8      1    952      7 (  0.73)     0  0    0   0   0   0     0 (0.00)   11    2 (28.57)
 7      6    958      6 (  0.63)     0  0    0   2   0   0     2 (33.33)   13    2 (33.33)
-1    638   1596      0 (  0.00)    98  0    0  29   4   2    35 (5.49)   48    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     492      492        2
  9       3      495        3
 11       2      497        4
 12       4      501        5
 14       2      503        5
 15       4      507        7
 16       6      513        5
 17       8      521        7
 18       1      522        7
 19       4      526        6
 21       1      527        7
 23       8      535        7
 24       2      537        8
 26       2      539        9
 27       7      546       10
 29       6      552       11
 30       1      553       11
 31       1      554       11
 32       2      556       12
 33      11      567       11
 34       5      572       14
 35       4      576       17
 36       3      579       17
 37       5      584       18
 38       7      591       20
 39       4      595       21
 40       2      597       21
 41       3      600       21
 42      29      629       22
 43       9      638       24
 44      18      656       25
 45       4      660       25
 46       4      664       26
 47       5      669       27
 48      14      683       33
 49       3      686       33
 50      19      705       33
 51       6      711       33
 52      11      722       35
 53       5      727       37
 54      12      739       36
 55       9      748       40
 56      19      767       38
 57      17      784       38
 58      10      794       41
 59      22      816       38
 60      14      830       39
 61      11      841       39
 62       8      849       37
 63      14      863       37
 64       5      868       36
 65       9      877       35
 66      14      891       37
 67      15      906       31
 68       8      914       29
 70      14      928       28
 71       7      935       25
 72      11      946       20
 74       8      954       20
 75       9      963       14
 76       3      966       13
 77       3      969       12
 79       9      978        9
 80       2      980        8
 81       4      984        5
 83       5      989        2
 86       1      990        1

SS region: 388 (39.19%), 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):
   31     -3.7  [-2.1,  0.0]  (2, 0)

Read/contig discrepancies (* = higher-quality):
    79  S   C ah100109r1      (0)/(0)  64 GCTTCCTTTTAAAGGGA / GAAGGCGCTATCCATA
     7  S     ah100109f1      (0)/(0)  6 CAT / CTT
    15  S     ah100109f1      (0)/(0)  14 CAT / CCT
    31  I     ah100109f1      (0)/(0)  27 AAAAAT / ATAATGT
    36  S     ah100109f1      (0)/(0)  35 AAT / ACT
    42  S     ah100109f1      (0)/(0)  41 TAG / TCG
    92  S     ah100109f1      (0)/(0)  91 CAA / CCA

0 HQ discrepancies in 0 reads.
7 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; 977 bp (untrimmed), 882 (trimmed).  Isolated contig.
      1   970 ag080109f1    860 (  0)  1.16 1.27 0.11    0 ( 91)   24 ( 81) 
C    65  1022 ag080109r1    889 (  0)  0.55 0.11 0.11    0 ( 27)   45 (127) 

Overall discrep rates (%):             0.86 0.70 0.11

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90     362  37.1     362  37.1    0.00
 89       6   0.6     368  37.7    0.00
 88      13   1.3     381  39.0    0.00
 87       5   0.5     386  39.5    0.00
 86      11   1.1     397  40.6    0.00
 85      16   1.6     413  42.3    0.00
 84       5   0.5     418  42.8    0.00
 83       4   0.4     422  43.2    0.00
 82       2   0.2     424  43.4    0.00
 81      18   1.8     442  45.2    0.00
 80      16   1.6     458  46.9    0.00
 79       5   0.5     463  47.4    0.00
 78       7   0.7     470  48.1    0.00
 77       7   0.7     477  48.8    0.00
 76      10   1.0     487  49.8    0.00
 75      12   1.2     499  51.1    0.00
 74      12   1.2     511  52.3    0.00
 73       8   0.8     519  53.1    0.00
 72       3   0.3     522  53.4    0.00
 71      23   2.4     545  55.8    0.00
 70       8   0.8     553  56.6    0.00
 69       6   0.6     559  57.2    0.00
 68       8   0.8     567  58.0    0.00
 67       6   0.6     573  58.6    0.00
 66      19   1.9     592  60.6    0.00
 65      15   1.5     607  62.1    0.00
 64       7   0.7     614  62.8    0.00
 63       9   0.9     623  63.8    0.00
 62       1   0.1     624  63.9    0.00
 60       4   0.4     628  64.3    0.00
 59      11   1.1     639  65.4    0.00
 58       8   0.8     647  66.2    0.00
 57       3   0.3     650  66.5    0.00
 56      56   5.7     706  72.3    0.00
 55       6   0.6     712  72.9    0.00
 54       2   0.2     714  73.1    0.00
 53       2   0.2     716  73.3    0.00
 52       3   0.3     719  73.6    0.00
 51      55   5.6     774  79.2    0.00
 50       2   0.2     776  79.4    0.00
 49       5   0.5     781  79.9    0.00
 48       6   0.6     787  80.6    0.00
 47       5   0.5     792  81.1    0.00
 46       7   0.7     799  81.8    0.00
 45      16   1.6     815  83.4    0.00
 43       6   0.6     821  84.0    0.00
 41       1   0.1     822  84.1    0.00
 40      16   1.6     838  85.8    0.00
 39       2   0.2     840  86.0    0.00
 37       3   0.3     843  86.3    0.00
 35       9   0.9     852  87.2    0.01
 34       4   0.4     856  87.6    0.01
 33       1   0.1     857  87.7    0.01
 32       2   0.2     859  87.9    0.01
 31       1   0.1     860  88.0    0.01
 28       1   0.1     861  88.1    0.01
 27       6   0.6     867  88.7    0.03
 26       1   0.1     868  88.8    0.03
 23       1   0.1     869  88.9    0.03
 21       1   0.1     870  89.0    0.04
 19       1   0.1     871  89.2    0.05
 16       1   0.1     872  89.3    0.08
 15       1   0.1     873  89.4    0.11
 14       2   0.2     875  89.6    0.19
 12       1   0.1     876  89.7    0.25
 11       3   0.3     879  90.0    0.49
 10       3   0.3     882  90.3    0.79
 -1      95   9.7     977 100.0   95.79   (quality -1 = terminal quality 0)

Avg. full length: 977.0, trimmed (qual > -1): 882.0
Avg. quality: 66.1 per base

Initial, terminal qual 0 segments:  1-64, 947-977

Regions of LLR- adjusted quality < 2.0:
1-64, 80-86, 116-120, 947-977, 

4 regions, avg size 26.8, avg spacing 244.2

First_start: 92, last_end: 895

Slack, # used pairs (max_score), unused
 0     1  (19.1)     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+
  947 - right       31+      ag080109f1   (   1)    No            976+

Bottom strand: 
 left -    64       64+      ag080109r1   (1022)    No           1022+
  978 - 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    639    639   1852 (100.00)     0  0    0   0   0   0     0 (0.00)    0   31 (1.67)
51    263    902   1213 ( 65.50)     0  0    0   0   0   0     0 (0.00)    0   31 (2.56)
50      8    910    950 ( 51.30)     0  0    0   0   0   0     0 (0.00)    0   31 (3.26)
48     19    929    942 ( 50.86)     0  0    0   0   0   0     0 (0.00)    0   31 (3.29)
47      2    931    923 ( 49.84)     0  0    0   0   0   0     0 (0.00)    0   31 (3.36)
46     30    961    921 ( 49.73)     0  0    0   0   0   0     0 (0.00)    0   31 (3.37)
45     56   1017    891 ( 48.11)     0  0    0   0   0   0     0 (0.00)    0   31 (3.48)
44      6   1023    835 ( 45.09)     0  0    0   0   0   0     0 (0.00)    0   31 (3.71)
43     33   1056    829 ( 44.76)     0  0    0   0   0   0     0 (0.00)    0   31 (3.74)
42     42   1098    796 ( 42.98)     0  0    0   0   0   0     0 (0.00)    0   31 (3.89)
40    113   1211    754 ( 40.71)     0  0    0   0   0   0     0 (0.00)    0   31 (4.11)
39      5   1216    641 ( 34.61)     0  0    0   0   0   0     0 (0.00)    0   31 (4.84)
38      6   1222    636 ( 34.34)     0  0    0   0   0   0     0 (0.00)    0   31 (4.87)
37     11   1233    630 ( 34.02)     0  0    0   0   0   0     0 (0.00)    0   31 (4.92)
36      9   1242    619 ( 33.42)     0  0    0   0   0   0     0 (0.00)    0   31 (5.01)
35     27   1269    610 ( 32.94)     0  0    0   0   0   0     0 (0.00)    0   31 (5.08)
34     20   1289    583 ( 31.48)     0  0    0   0   0   0     0 (0.00)    0   31 (5.32)
33      8   1297    563 ( 30.40)     0  0    0   0   0   0     0 (0.00)    0   31 (5.51)
32     19   1316    555 ( 29.97)     0  0    0   0   0   0     0 (0.00)    0   31 (5.59)
31      5   1321    536 ( 28.94)     0  0    0   0   0   0     0 (0.00)    0   31 (5.78)
30      6   1327    531 ( 28.67)     0  0    0   0   0   0     0 (0.00)    0   31 (5.84)
29     23   1350    525 ( 28.35)     0  0    0   0   0   0     0 (0.00)    0   31 (5.90)
28      6   1356    502 ( 27.11)     0  0    0   0   0   0     0 (0.00)    0   31 (6.18)
27     12   1368    496 ( 26.78)     0  0    0   0   0   0     0 (0.00)    0   31 (6.25)
26      2   1370    484 ( 26.13)     0  0    0   0   0   0     0 (0.00)    0   31 (6.40)
25     30   1400    482 ( 26.03)     0  0    0   0   0   0     0 (0.00)    0   31 (6.43)
24     14   1414    452 ( 24.41)     0  0    0   0   0   0     0 (0.00)    0   31 (6.86)
23      9   1423    438 ( 23.65)     0  0    0   0   0   0     0 (0.00)    0   31 (7.08)
22      7   1430    429 ( 23.16)     0  0    0   0   0   0     0 (0.00)    0   31 (7.23)
21     11   1441    422 ( 22.79)     0  0    0   0   0   0     0 (0.00)    0   31 (7.35)
20      7   1448    411 ( 22.19)     0  0    0   0   0   0     0 (0.00)    0   31 (7.54)
19     19   1467    404 ( 21.81)     0  0    0   0   0   0     0 (0.00)    0   31 (7.67)
18     14   1481    385 ( 20.79)     0  0    0   0   0   0     0 (0.00)    0   31 (8.05)
17     13   1494    371 ( 20.03)     0  0    0   0   0   0     0 (0.00)    0   31 (8.36)
16     21   1515    358 ( 19.33)     0  0    0   0   0   0     0 (0.00)    0   31 (8.66)
15     18   1533    337 ( 18.20)     0  0    0   0   0   0     0 (0.00)    0   31 (9.20)
14     11   1544    319 ( 17.22)     0  0    0   0   0   0     0 (0.00)    0   31 (9.72)
13     32   1576    308 ( 16.63)     0  0    0   1   1   0     2 (6.25)    2   31 (10.06)
12     29   1605    276 ( 14.90)     0  0    0   1   1   0     2 (6.90)    4   29 (10.51)
11     43   1648    247 ( 13.34)     0  0    0   3   3   0     6 (13.95)   10   27 (10.93)
10     49   1697    204 ( 11.02)     0  0    0   2   0   0     2 (4.08)   12   21 (10.29)
 9     66   1763    155 (  8.37)     0  0    0   3   3   1     7 (10.61)   19   19 (12.26)
 8     35   1798     89 (  4.81)     0  0    0   1   1   0     2 (5.71)   21   12 (13.48)
 7     34   1832     54 (  2.92)     0  0    0   5   1   1     7 (20.59)   28   10 (18.52)
 6     20   1852     20 (  1.08)     0  0    0   0   3   0     3 (15.00)   31    3 (15.00)
-1     18   1870      0 (  0.00)    24  0    0   0   0   0     0 (0.00)   31    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    724    724   1691 (100.00)     0  0    0   0   0   0     0 (0.00)    0   11 (0.65)
89     12    736    967 ( 57.19)     0  0    0   0   0   0     0 (0.00)    0   11 (1.14)
88     26    762    955 ( 56.48)     0  0    0   0   0   0     0 (0.00)    0   11 (1.15)
87     10    772    929 ( 54.94)     0  0    0   0   0   0     0 (0.00)    0   11 (1.18)
86     22    794    919 ( 54.35)     0  0    0   0   0   0     0 (0.00)    0   11 (1.20)
85     31    825    897 ( 53.05)     0  0    0   0   0   0     0 (0.00)    0   11 (1.23)
84     10    835    866 ( 51.21)     0  0    0   0   0   0     0 (0.00)    0   11 (1.27)
83      8    843    856 ( 50.62)     0  0    0   0   0   0     0 (0.00)    0   11 (1.29)
82      4    847    848 ( 50.15)     0  0    0   0   0   0     0 (0.00)    0   11 (1.30)
81     35    882    844 ( 49.91)     0  0    0   0   0   0     0 (0.00)    0   11 (1.30)
80     30    912    809 ( 47.84)     0  0    0   0   0   0     0 (0.00)    0   11 (1.36)
79     10    922    779 ( 46.07)     0  0    0   0   0   0     0 (0.00)    0   11 (1.41)
78     14    936    769 ( 45.48)     0  0    0   0   0   0     0 (0.00)    0   11 (1.43)
77     14    950    755 ( 44.65)     0  0    0   0   0   0     0 (0.00)    0   11 (1.46)
76     20    970    741 ( 43.82)     0  0    0   0   0   0     0 (0.00)    0   11 (1.48)
75     23    993    721 ( 42.64)     0  0    0   0   0   0     0 (0.00)    0   11 (1.53)
74     22   1015    698 ( 41.28)     0  0    0   0   0   0     0 (0.00)    0   11 (1.58)
73     11   1026    676 ( 39.98)     0  0    0   0   0   0     0 (0.00)    0   11 (1.63)
72      3   1029    665 ( 39.33)     0  0    0   0   0   0     0 (0.00)    0   11 (1.65)
71     27   1056    662 ( 39.15)     0  0    0   0   0   0     0 (0.00)    0   11 (1.66)
70     16   1072    635 ( 37.55)     0  0    0   0   0   0     0 (0.00)    0   11 (1.73)
69     10   1082    619 ( 36.61)     0  0    0   0   0   0     0 (0.00)    0   11 (1.78)
68     11   1093    609 ( 36.01)     0  0    0   0   0   0     0 (0.00)    0   11 (1.81)
67     13   1106    598 ( 35.36)     0  0    0   0   0   0     0 (0.00)    0   11 (1.84)
66     22   1128    585 ( 34.59)     0  0    0   0   0   0     0 (0.00)    0   11 (1.88)
65     19   1147    563 ( 33.29)     0  0    0   0   0   0     0 (0.00)    0   11 (1.95)
64     10   1157    544 ( 32.17)     0  0    0   0   0   0     0 (0.00)    0   11 (2.02)
63      9   1166    534 ( 31.58)     0  0    0   0   0   0     0 (0.00)    0   11 (2.06)
62      1   1167    525 ( 31.05)     0  0    0   0   0   0     0 (0.00)    0   11 (2.10)
61      1   1168    524 ( 30.99)     0  0    0   0   0   0     0 (0.00)    0   11 (2.10)
60      4   1172    523 ( 30.93)     0  0    0   0   0   0     0 (0.00)    0   11 (2.10)
59     16   1188    519 ( 30.69)     0  0    0   0   0   0     0 (0.00)    0   11 (2.12)
58      8   1196    503 ( 29.75)     0  0    0   0   0   0     0 (0.00)    0   11 (2.19)
57      3   1199    495 ( 29.27)     0  0    0   0   0   0     0 (0.00)    0   11 (2.22)
56    124   1323    492 ( 29.10)     0  0    0   0   0   0     0 (0.00)    0   11 (2.24)
55      7   1330    368 ( 21.76)     0  0    0   0   0   0     0 (0.00)    0   11 (2.99)
54      5   1335    361 ( 21.35)     0  0    0   0   0   0     0 (0.00)    0   11 (3.05)
53      5   1340    356 ( 21.05)     0  0    0   0   0   0     0 (0.00)    0   11 (3.09)
52      3   1343    351 ( 20.76)     0  0    0   0   0   0     0 (0.00)    0   11 (3.13)
51     75   1418    348 ( 20.58)     0  0    0   0   0   0     0 (0.00)    0   11 (3.16)
50      2   1420    273 ( 16.14)     0  0    0   0   0   0     0 (0.00)    0   11 (4.03)
49      5   1425    271 ( 16.03)     0  0    0   0   0   0     0 (0.00)    0   11 (4.06)
48      6   1431    266 ( 15.73)     0  0    0   0   0   0     0 (0.00)    0   11 (4.14)
47      5   1436    260 ( 15.38)     0  0    0   0   0   0     0 (0.00)    0   11 (4.23)
46     13   1449    255 ( 15.08)     0  0    0   0   0   0     0 (0.00)    0   11 (4.31)
45     17   1466    242 ( 14.31)     0  0    0   0   0   0     0 (0.00)    0   11 (4.55)
44      4   1470    225 ( 13.31)     0  0    0   0   0   0     0 (0.00)    0   11 (4.89)
43      7   1477    221 ( 13.07)     0  0    0   0   0   0     0 (0.00)    0   11 (4.98)
42      6   1483    214 ( 12.66)     0  0    0   0   0   0     0 (0.00)    0   11 (5.14)
41      1   1484    208 ( 12.30)     0  0    0   0   0   0     0 (0.00)    0   11 (5.29)
40     34   1518    207 ( 12.24)     0  0    0   0   0   0     0 (0.00)    0   11 (5.31)
39      3   1521    173 ( 10.23)     0  0    0   0   0   0     0 (0.00)    0   11 (6.36)
38      1   1522    170 ( 10.05)     0  0    0   0   0   0     0 (0.00)    0   11 (6.47)
37      3   1525    169 (  9.99)     0  0    0   0   0   0     0 (0.00)    0   11 (6.51)
35      9   1534    166 (  9.82)     0  0    0   0   0   0     0 (0.00)    0   11 (6.63)
34      4   1538    157 (  9.28)     0  0    0   0   0   0     0 (0.00)    0   11 (7.01)
33      7   1545    153 (  9.05)     0  0    0   0   0   0     0 (0.00)    0   11 (7.19)
32      6   1551    146 (  8.63)     0  0    0   0   0   0     0 (0.00)    0   11 (7.53)
31      5   1556    140 (  8.28)     0  0    0   0   0   0     0 (0.00)    0   11 (7.86)
30      3   1559    135 (  7.98)     0  0    0   0   0   0     0 (0.00)    0   11 (8.15)
28      9   1568    132 (  7.81)     0  0    0   0   0   0     0 (0.00)    0   11 (8.33)
27      9   1577    123 (  7.27)     0  0    0   0   0   0     0 (0.00)    0   11 (8.94)
26      7   1584    114 (  6.74)     0  0    0   0   0   0     0 (0.00)    0   11 (9.65)
25      7   1591    107 (  6.33)     0  0    0   0   0   0     0 (0.00)    0   11 (10.28)
24      6   1597    100 (  5.91)     0  0    0   0   0   0     0 (0.00)    0   11 (11.00)
23      7   1604     94 (  5.56)     0  0    0   0   0   0     0 (0.00)    0   11 (11.70)
22      1   1605     87 (  5.14)     0  0    0   0   0   0     0 (0.00)    0   11 (12.64)
21      4   1609     86 (  5.09)     0  0    0   0   0   0     0 (0.00)    0   11 (12.79)
19      2   1611     82 (  4.85)     0  0    0   0   0   0     0 (0.00)    0   11 (13.41)
17      1   1612     80 (  4.73)     0  0    0   0   0   0     0 (0.00)    0   11 (13.75)
16      2   1614     79 (  4.67)     0  0    0   0   0   0     0 (0.00)    0   11 (13.92)
15      2   1616     77 (  4.55)     0  0    0   0   0   0     0 (0.00)    0   11 (14.29)
14      3   1619     75 (  4.44)     0  0    0   0   0   0     0 (0.00)    0   11 (14.67)
13     12   1631     72 (  4.26)     0  0    0   1   1   0     2 (16.67)    2   11 (15.28)
12      7   1638     60 (  3.55)     0  0    0   1   0   0     1 (14.29)    3    9 (15.00)
11      8   1646     53 (  3.13)     0  0    0   0   0   0     0 (0.00)    3    8 (15.09)
10     14   1660     45 (  2.66)     0  0    0   0   0   0     0 (0.00)    3    8 (17.78)
 9     13   1673     31 (  1.83)     0  0    0   2   1   0     3 (23.08)    6    8 (25.81)
 8      6   1679     18 (  1.06)     0  0    0   0   1   0     1 (16.67)    7    5 (27.78)
 7      5   1684     12 (  0.71)     0  0    0   2   0   0     2 (40.00)    9    4 (33.33)
 6      7   1691      7 (  0.41)     0  0    0   0   2   0     2 (28.57)   11    2 (28.57)
-1    179   1870      0 (  0.00)    24  0    0  10   8   2    20 (11.17)   31    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      95       95        2
 10       3       98        5
 11       3      101        5
 12       1      102        5
 14       2      104        6
 15       1      105        5
 16       1      106        4
 19       1      107        4
 21       1      108        4
 23       1      109        4
 26       1      110        4
 27       6      116        4
 28       1      117        4
 31       1      118        4
 32       2      120        4
 33       1      121        4
 34       4      125        5
 35       9      134        7
 37       3      137        7
 39       2      139        8
 40      16      155        9
 41       1      156        9
 43       6      162       10
 45      16      178       13
 46       7      185       15
 47       5      190       17
 48       6      196       15
 49       5      201       17
 50       2      203       16
 51      55      258       16
 52       3      261       17
 53       2      263       16
 54       2      265       15
 55       6      271       16
 56      56      327       12
 57       3      330       13
 58       8      338       15
 59      11      349       14
 60       4      353       14
 62       1      354       14
 63       9      363       17
 64       7      370       20
 65      15      385       19
 66      19      404       19
 67       6      410       18
 68       8      418       17
 69       6      424       17
 70       8      432       19
 71      23      455       23
 72       3      458       20
 73       8      466       18
 74      12      478       19
 75      12      490       19
 76      10      500       20
 77       7      507       19
 78       7      514       21
 79       5      519       21
 80      16      535       20
 81      18      553       18
 82       2      555       17
 83       4      559       17
 84       5      564       16
 85      16      580       12
 86      11      591       17
 87       5      596       19
 88      13      609       19
 89       6      615       17
 90     362      977        1

SS region: 95 (9.72%), 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): 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 7.  2 reads; 314 bp (untrimmed), 314 (trimmed).
C  -596   362 ac100109r1    312 (282)  0.00 0.00 0.00  597 (597)   48 ( 48) 
     -9   976 ac100109f1    271 (251)  2.87 0.32 0.64   10 ( 10)  662 (662) 

Overall discrep rates (%):             1.43 0.16 0.32

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90     179  57.0     179  57.0    0.00
 89       1   0.3     180  57.3    0.00
 88       5   1.6     185  58.9    0.00
 87       3   1.0     188  59.9    0.00
 85       2   0.6     190  60.5    0.00
 84       5   1.6     195  62.1    0.00
 83       2   0.6     197  62.7    0.00
 82       6   1.9     203  64.6    0.00
 81       8   2.5     211  67.2    0.00
 80       3   1.0     214  68.2    0.00
 79       1   0.3     215  68.5    0.00
 78       4   1.3     219  69.7    0.00
 77       2   0.6     221  70.4    0.00
 76       6   1.9     227  72.3    0.00
 74       3   1.0     230  73.2    0.00
 72       3   1.0     233  74.2    0.00
 71      18   5.7     251  79.9    0.00
 66       8   2.5     259  82.5    0.00
 61       3   1.0     262  83.4    0.00
 56      23   7.3     285  90.8    0.00
 51      18   5.7     303  96.5    0.00
 46       2   0.6     305  97.1    0.00
 45       2   0.6     307  97.8    0.00
 42       4   1.3     311  99.0    0.00
 41       3   1.0     314 100.0    0.00   (quality -1 = terminal quality 0)

Avg. full length: 314.0, trimmed (qual > -1): 314.0
Avg. quality: 80.1 per base

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

Regions of LLR- adjusted quality < 2.0:


1 regions, avg size 0.0, avg spacing 314.0

First_start: 1, last_end: 314

Slack, # used pairs (max_score), unused
 0     1  ( 6.5)     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+
  315 - right        0+      ac100109f1   (  -9)    No            323+

Bottom strand: 
 left -     0        0+      ac100109r1   ( 362)    Yes           362+
  315 - 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    248    248    627 (100.00)     0  0    0   0   0   0     0 (0.00)    0   12 (1.91)
51     81    329    379 ( 60.45)     0  0    0   0   0   0     0 (0.00)    0   12 (3.17)
50     22    351    298 ( 47.53)     0  0    0   0   0   0     0 (0.00)    0   12 (4.03)
48      6    357    276 ( 44.02)     0  0    0   0   0   0     0 (0.00)    0   12 (4.35)
47      3    360    270 ( 43.06)     0  0    0   0   0   0     0 (0.00)    0   12 (4.44)
46     16    376    267 ( 42.58)     0  0    0   0   0   0     0 (0.00)    0   12 (4.49)
45     18    394    251 ( 40.03)     0  0    0   0   0   0     0 (0.00)    0   12 (4.78)
44     13    407    233 ( 37.16)     0  0    0   0   0   0     0 (0.00)    0   12 (5.15)
43     13    420    220 ( 35.09)     0  0    0   0   0   0     0 (0.00)    0   12 (5.45)
42     20    440    207 ( 33.01)     0  0    0   0   0   0     0 (0.00)    0   12 (5.80)
41      6    446    187 ( 29.82)     0  0    0   0   0   0     0 (0.00)    0   12 (6.42)
40     41    487    181 ( 28.87)     0  0    0   0   0   0     0 (0.00)    0   12 (6.63)
39      4    491    140 ( 22.33)     0  0    0   0   0   0     0 (0.00)    0   12 (8.57)
38      0    491    136 ( 21.69)     0  0    0   0   0   0     0 (0.00)    0   12 (8.82)
37     12    503    136 ( 21.69)     0  0    0   0   0   0     0 (0.00)    0   12 (8.82)
36      4    507    124 ( 19.78)     0  0    0   0   0   0     0 (0.00)    0   12 (9.68)
35      9    516    120 ( 19.14)     0  0    0   0   0   0     0 (0.00)    0   12 (10.00)
34      9    525    111 ( 17.70)     0  0    0   0   0   0     0 (0.00)    0   12 (10.81)
33      2    527    102 ( 16.27)     0  0    0   0   0   0     0 (0.00)    0   12 (11.76)
32      1    528    100 ( 15.95)     0  0    0   0   0   0     0 (0.00)    0   12 (12.00)
31      1    529     99 ( 15.79)     0  0    0   0   0   0     0 (0.00)    0   12 (12.12)
30      1    530     98 ( 15.63)     0  0    0   0   0   0     0 (0.00)    0   12 (12.24)
29      4    534     97 ( 15.47)     0  0    0   0   0   0     0 (0.00)    0   12 (12.37)
28      3    537     93 ( 14.83)     0  0    0   0   0   0     0 (0.00)    0   12 (12.90)
27      2    539     90 ( 14.35)     0  0    0   0   0   0     0 (0.00)    0   12 (13.33)
26      6    545     88 ( 14.04)     0  0    0   0   0   0     0 (0.00)    0   12 (13.64)
25     12    557     82 ( 13.08)     0  0    0   0   0   0     0 (0.00)    0   12 (14.63)
24      3    560     70 ( 11.16)     0  0    0   0   0   0     0 (0.00)    0   12 (17.14)
23      1    561     67 ( 10.69)     0  0    0   0   0   0     0 (0.00)    0   12 (17.91)
22      5    566     66 ( 10.53)     0  0    0   0   0   0     0 (0.00)    0   12 (18.18)
21      2    568     61 (  9.73)     0  0    0   0   0   0     0 (0.00)    0   12 (19.67)
20      2    570     59 (  9.41)     0  0    0   0   0   0     0 (0.00)    0   12 (20.34)
19      3    573     57 (  9.09)     0  0    0   0   0   0     0 (0.00)    0   12 (21.05)
18      2    575     54 (  8.61)     0  0    0   0   0   0     0 (0.00)    0   12 (22.22)
17      3    578     52 (  8.29)     0  0    0   0   0   0     0 (0.00)    0   12 (23.08)
16      2    580     49 (  7.81)     0  0    0   0   0   0     0 (0.00)    0   12 (24.49)
15      2    582     47 (  7.50)     0  0    0   0   0   0     0 (0.00)    0   12 (25.53)
13      7    589     45 (  7.18)     0  0    0   1   0   0     1 (14.29)    1   12 (26.67)
12      6    595     38 (  6.06)     0  0    0   0   0   0     0 (0.00)    1   11 (28.95)
11      3    598     32 (  5.10)     0  0    0   0   0   0     0 (0.00)    1   11 (34.38)
 9     13    611     29 (  4.63)     0  0    0   4   0   2     6 (46.15)    7   11 (37.93)
 8      7    618     16 (  2.55)     0  0    0   2   0   0     2 (28.57)    9    5 (31.25)
 7      3    621      9 (  1.44)     0  0    0   0   0   0     0 (0.00)    9    3 (33.33)
 6      2    623      6 (  0.96)     0  0    0   0   1   0     1 (50.00)   10    3 (50.00)
 4      4    627      4 (  0.64)     0  0    0   2   0   0     2 (50.00)   12    2 (50.00)
-1      0    627      0 (  0.00)     0  0    0   0   0   0     0 (0.00)   12    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    358    358    627 (100.00)     0  0    0   0   0   0     0 (0.00)    0   12 (1.91)
89      2    360    269 ( 42.90)     0  0    0   0   0   0     0 (0.00)    0   12 (4.46)
88     10    370    267 ( 42.58)     0  0    0   0   0   0     0 (0.00)    0   12 (4.49)
87      6    376    257 ( 40.99)     0  0    0   0   0   0     0 (0.00)    0   12 (4.67)
85      4    380    251 ( 40.03)     0  0    0   0   0   0     0 (0.00)    0   12 (4.78)
84     10    390    247 ( 39.39)     0  0    0   0   0   0     0 (0.00)    0   12 (4.86)
83      4    394    237 ( 37.80)     0  0    0   0   0   0     0 (0.00)    0   12 (5.06)
82     12    406    233 ( 37.16)     0  0    0   0   0   0     0 (0.00)    0   12 (5.15)
81     16    422    221 ( 35.25)     0  0    0   0   0   0     0 (0.00)    0   12 (5.43)
80      6    428    205 ( 32.70)     0  0    0   0   0   0     0 (0.00)    0   12 (5.85)
79      2    430    199 ( 31.74)     0  0    0   0   0   0     0 (0.00)    0   12 (6.03)
78      8    438    197 ( 31.42)     0  0    0   0   0   0     0 (0.00)    0   12 (6.09)
77      4    442    189 ( 30.14)     0  0    0   0   0   0     0 (0.00)    0   12 (6.35)
76     12    454    185 ( 29.51)     0  0    0   0   0   0     0 (0.00)    0   12 (6.49)
74      6    460    173 ( 27.59)     0  0    0   0   0   0     0 (0.00)    0   12 (6.94)
72      6    466    167 ( 26.63)     0  0    0   0   0   0     0 (0.00)    0   12 (7.19)
71     20    486    161 ( 25.68)     0  0    0   0   0   0     0 (0.00)    0   12 (7.45)
66      8    494    141 ( 22.49)     0  0    0   0   0   0     0 (0.00)    0   12 (8.51)
62      1    495    133 ( 21.21)     0  0    0   0   0   0     0 (0.00)    0   12 (9.02)
61      3    498    132 ( 21.05)     0  0    0   0   0   0     0 (0.00)    0   12 (9.09)
59      1    499    129 ( 20.57)     0  0    0   0   0   0     0 (0.00)    0   12 (9.30)
56     23    522    128 ( 20.41)     0  0    0   0   0   0     0 (0.00)    0   12 (9.38)
55      1    523    105 ( 16.75)     0  0    0   0   0   0     0 (0.00)    0   12 (11.43)
51     20    543    104 ( 16.59)     0  0    0   0   0   0     0 (0.00)    0   12 (11.54)
49      2    545     84 ( 13.40)     0  0    0   0   0   0     0 (0.00)    0   12 (14.29)
47      1    546     82 ( 13.08)     0  0    0   0   0   0     0 (0.00)    0   12 (14.63)
46      2    548     81 ( 12.92)     0  0    0   0   0   0     0 (0.00)    0   12 (14.81)
45      3    551     79 ( 12.60)     0  0    0   0   0   0     0 (0.00)    0   12 (15.19)
44      1    552     76 ( 12.12)     0  0    0   0   0   0     0 (0.00)    0   12 (15.79)
42      6    558     75 ( 11.96)     0  0    0   0   0   0     0 (0.00)    0   12 (16.00)
41      4    562     69 ( 11.00)     0  0    0   0   0   0     0 (0.00)    0   12 (17.39)
40      3    565     65 ( 10.37)     0  0    0   0   0   0     0 (0.00)    0   12 (18.46)
39      2    567     62 (  9.89)     0  0    0   0   0   0     0 (0.00)    0   12 (19.35)
37      2    569     60 (  9.57)     0  0    0   0   0   0     0 (0.00)    0   12 (20.00)
36      1    570     58 (  9.25)     0  0    0   0   0   0     0 (0.00)    0   12 (20.69)
35      1    571     57 (  9.09)     0  0    0   0   0   0     0 (0.00)    0   12 (21.05)
34      1    572     56 (  8.93)     0  0    0   0   0   0     0 (0.00)    0   12 (21.43)
33      1    573     55 (  8.77)     0  0    0   0   0   0     0 (0.00)    0   12 (21.82)
32      1    574     54 (  8.61)     0  0    0   0   0   0     0 (0.00)    0   12 (22.22)
30      1    575     53 (  8.45)     0  0    0   0   0   0     0 (0.00)    0   12 (22.64)
28      2    577     52 (  8.29)     0  0    0   0   0   0     0 (0.00)    0   12 (23.08)
27      3    580     50 (  7.97)     0  0    0   0   0   0     0 (0.00)    0   12 (24.00)
22      1    581     47 (  7.50)     0  0    0   0   0   0     0 (0.00)    0   12 (25.53)
19      2    583     46 (  7.34)     0  0    0   0   0   0     0 (0.00)    0   12 (26.09)
18      1    584     44 (  7.02)     0  0    0   0   0   0     0 (0.00)    0   12 (27.27)
17      2    586     43 (  6.86)     0  0    0   0   0   0     0 (0.00)    0   12 (27.91)
16      2    588     41 (  6.54)     0  0    0   0   0   0     0 (0.00)    0   12 (29.27)
13      5    593     39 (  6.22)     0  0    0   1   0   0     1 (20.00)    1   12 (30.77)
12      3    596     34 (  5.42)     0  0    0   0   0   0     0 (0.00)    1   11 (32.35)
11      3    599     31 (  4.94)     0  0    0   0   0   0     0 (0.00)    1   11 (35.48)
 9     13    612     28 (  4.47)     0  0    0   4   0   2     6 (46.15)    7   11 (39.29)
 8      7    619     15 (  2.39)     0  0    0   2   0   0     2 (28.57)    9    5 (33.33)
 7      2    621      8 (  1.28)     0  0    0   0   0   0     0 (0.00)    9    3 (37.50)
 6      2    623      6 (  0.96)     0  0    0   0   1   0     1 (50.00)   10    3 (50.00)
 4      4    627      4 (  0.64)     0  0    0   2   0   0     2 (50.00)   12    2 (50.00)
-1      0    627      0 (  0.00)     0  0    0   0   0   0     0 (0.00)   12    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
 41       3        3        1
 42       4        7        2
 45       2        9        2
 46       2       11        2
 51      18       29        6
 56      23       52        6
 61       3       55        7
 66       8       63        8
 71      18       81        7
 72       3       84        8
 74       3       87        9
 76       6       93       12
 77       2       95       11
 78       4       99       13
 79       1      100       14
 80       3      103       15
 81       8      111       12
 82       6      117       12
 83       2      119       11
 84       5      124       11
 85       2      126       10
 87       3      129       10
 88       5      134       11
 89       1      135       11
 90     179      314        1

SS region: 0 (0.00%), 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): 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 1- 314

Contig 8.  2 reads; 1642 bp (untrimmed), 1479 (trimmed).  Isolated contig.
      1   955 aa090109f1    863 (  0)  0.94 1.47 0.10    0 (684)    2 ( 70) 
C   685  1642 aa090109r1    934 (  0)  0.21 0.10 0.21    0 (  0)    0 (750) 

Overall discrep rates (%):             0.58 0.78 0.16

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56     637  38.8     637  38.8    0.00
 51     229  13.9     866  52.7    0.00
 50      25   1.5     891  54.3    0.00
 49       1   0.1     892  54.3    0.00
 48      16   1.0     908  55.3    0.00
 47       2   0.1     910  55.4    0.00
 46      17   1.0     927  56.5    0.00
 45      52   3.2     979  59.6    0.01
 44      26   1.6    1005  61.2    0.01
 43      21   1.3    1026  62.5    0.01
 42      64   3.9    1090  66.4    0.01
 41       2   0.1    1092  66.5    0.01
 40      51   3.1    1143  69.6    0.02
 39       3   0.2    1146  69.8    0.02
 38      10   0.6    1156  70.4    0.02
 37      28   1.7    1184  72.1    0.02
 36       9   0.5    1193  72.7    0.03
 35      28   1.7    1221  74.4    0.04
 34      10   0.6    1231  75.0    0.04
 33      15   0.9    1246  75.9    0.05
 32      10   0.6    1256  76.5    0.05
 31       6   0.4    1262  76.9    0.06
 30       8   0.5    1270  77.3    0.07
 29      18   1.1    1288  78.4    0.09
 28      12   0.7    1300  79.2    0.11
 27      11   0.7    1311  79.8    0.13
 26      19   1.2    1330  81.0    0.18
 25      21   1.3    1351  82.3    0.24
 24      16   1.0    1367  83.3    0.31
 23      18   1.1    1385  84.3    0.40
 22      11   0.7    1396  85.0    0.47
 21       5   0.3    1401  85.3    0.51
 20      15   0.9    1416  86.2    0.66
 19      15   0.9    1431  87.1    0.85
 18       6   0.4    1437  87.5    0.94
 16       3   0.2    1440  87.7    1.02
 15       6   0.4    1446  88.1    1.21
 14       7   0.4    1453  88.5    1.49
 13       1   0.1    1454  88.6    1.54
 12       2   0.1    1456  88.7    1.66
 11       7   0.4    1463  89.1    2.22
 10       3   0.2    1466  89.3    2.52
  9       9   0.5    1475  89.8    3.65
  8       3   0.2    1478  90.0    4.13
  7       1   0.1    1479  90.1    4.33
 -1     163   9.9    1642 100.0  167.33   (quality -1 = terminal quality 0)

Avg. full length: 1642.0, trimmed (qual > -1): 1479.0
Avg. quality: 41.7 per base

Initial, terminal qual 0 segments:  1-83, 1563-1642

Regions of LLR- adjusted quality < 2.0:
1-85, 109-121, 164-167, 599-601, 606-608, 669, 685, 691-701, 
739, 775-776, 780-785, 822-827, 845, 847-848, 865, 876, 
880, 893-896, 1563-1642, 

19 regions, avg size 11.9, avg spacing 86.4

First_start: 685, last_end: 892

Slack, # used pairs (max_score), unused
 1     0  ( 0.0)     0 ( 0.0)        1
 3     1  ( 5.6)     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+
  954 - right      689+      aa090109f1   (   1)    No           1641+

Bottom strand: 
 left -   684      684+      aa090109r1   (1642)    No           1642+
 1643 - 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    640    640   1860 (100.00)     0  0    0   0   0   0     0 (0.00)    0   29 (1.56)
51    236    876   1220 ( 65.59)     0  0    0   0   0   0     0 (0.00)    0   29 (2.38)
50     25    901    984 ( 52.90)     0  0    0   0   0   0     0 (0.00)    0   29 (2.95)
48     18    919    959 ( 51.56)     0  0    0   0   0   0     0 (0.00)    0   29 (3.02)
47      2    921    941 ( 50.59)     0  0    0   0   0   0     0 (0.00)    0   29 (3.08)
46     17    938    939 ( 50.48)     0  0    0   0   0   0     0 (0.00)    0   29 (3.09)
45     54    992    922 ( 49.57)     0  0    0   0   0   0     0 (0.00)    0   29 (3.15)
44     25   1017    868 ( 46.67)     0  0    0   0   0   0     0 (0.00)    0   29 (3.34)
43     22   1039    843 ( 45.32)     0  0    0   0   0   0     0 (0.00)    0   29 (3.44)
42     64   1103    821 ( 44.14)     0  0    0   0   0   0     0 (0.00)    0   29 (3.53)
41      2   1105    757 ( 40.70)     0  0    0   0   0   0     0 (0.00)    0   29 (3.83)
40     59   1164    755 ( 40.59)     0  0    0   0   0   0     0 (0.00)    0   29 (3.84)
39      3   1167    696 ( 37.42)     0  0    0   0   0   0     0 (0.00)    0   29 (4.17)
38      6   1173    693 ( 37.26)     0  0    0   0   0   0     0 (0.00)    0   29 (4.18)
37     31   1204    687 ( 36.94)     0  0    0   0   0   0     0 (0.00)    0   29 (4.22)
36      5   1209    656 ( 35.27)     0  0    0   0   0   0     0 (0.00)    0   29 (4.42)
35     24   1233    651 ( 35.00)     0  0    0   0   0   0     0 (0.00)    0   29 (4.45)
34     23   1256    627 ( 33.71)     0  0    0   0   0   0     0 (0.00)    0   29 (4.63)
33      8   1264    604 ( 32.47)     0  0    0   0   0   0     0 (0.00)    0   29 (4.80)
32     13   1277    596 ( 32.04)     0  0    0   0   0   0     0 (0.00)    0   29 (4.87)
31      8   1285    583 ( 31.34)     0  0    0   0   0   0     0 (0.00)    0   29 (4.97)
30      1   1286    575 ( 30.91)     0  0    0   0   0   0     0 (0.00)    0   29 (5.04)
29     21   1307    574 ( 30.86)     0  0    0   0   0   0     0 (0.00)    0   29 (5.05)
28     10   1317    553 ( 29.73)     0  0    0   0   0   0     0 (0.00)    0   29 (5.24)
27     11   1328    543 ( 29.19)     0  0    0   0   0   0     0 (0.00)    0   29 (5.34)
26      6   1334    532 ( 28.60)     0  0    0   0   0   0     0 (0.00)    0   29 (5.45)
25     23   1357    526 ( 28.28)     0  0    0   0   0   0     0 (0.00)    0   29 (5.51)
24     15   1372    503 ( 27.04)     0  0    0   0   0   0     0 (0.00)    0   29 (5.77)
23     16   1388    488 ( 26.24)     0  0    0   0   0   0     0 (0.00)    0   29 (5.94)
22     20   1408    472 ( 25.38)     0  0    0   0   0   0     0 (0.00)    0   29 (6.14)
21     14   1422    452 ( 24.30)     0  0    0   0   0   0     0 (0.00)    0   29 (6.42)
20     30   1452    438 ( 23.55)     0  0    0   0   0   0     0 (0.00)    0   29 (6.62)
19     28   1480    408 ( 21.94)     0  0    0   0   0   1     1 (3.57)    1   29 (7.11)
18     17   1497    380 ( 20.43)     0  0    0   0   0   0     0 (0.00)    1   28 (7.37)
17      5   1502    363 ( 19.52)     0  0    0   0   0   0     0 (0.00)    1   28 (7.71)
16     16   1518    358 ( 19.25)     0  0    0   0   0   0     0 (0.00)    1   28 (7.82)
15     21   1539    342 ( 18.39)     0  0    0   0   0   0     0 (0.00)    1   28 (8.19)
14     19   1558    321 ( 17.26)     0  0    0   0   0   0     0 (0.00)    1   28 (8.72)
13     28   1586    302 ( 16.24)     0  0    0   0   0   0     0 (0.00)    1   28 (9.27)
12     20   1606    274 ( 14.73)     0  0    0   0   0   0     0 (0.00)    1   28 (10.22)
11     62   1668    254 ( 13.66)     0  0    0   2   1   0     3 (4.84)    4   28 (11.02)
10     44   1712    192 ( 10.32)     0  0    0   1   0   0     1 (2.27)    5   25 (13.02)
 9     52   1764    148 (  7.96)     0  0    0   0   2   2     4 (7.69)    9   24 (16.22)
 8     55   1819     96 (  5.16)     0  0    0   3   4   0     7 (12.73)   16   20 (20.83)
 7     21   1840     41 (  2.20)     0  0    0   3   4   0     7 (33.33)   23   13 (31.71)
 6     19   1859     20 (  1.08)     0  0    0   2   4   0     6 (31.58)   29    6 (30.00)
 4      1   1860      1 (  0.05)     0  0    0   0   0   0     0 (0.00)   29    0 (0.00)
-1     63   1923      0 (  0.00)     2  0    0   0   0   0     0 (0.00)   29    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 (%)
56    637    637   1692 (100.00)     0  0    0   0   0   0     0 (0.00)    0   15 (0.89)
51    229    866   1055 ( 62.35)     0  0    0   0   0   0     0 (0.00)    0   15 (1.42)
50     25    891    826 ( 48.82)     0  0    0   0   0   0     0 (0.00)    0   15 (1.82)
49      1    892    801 ( 47.34)     0  0    0   0   0   0     0 (0.00)    0   15 (1.87)
48     16    908    800 ( 47.28)     0  0    0   0   0   0     0 (0.00)    0   15 (1.88)
47      2    910    784 ( 46.34)     0  0    0   0   0   0     0 (0.00)    0   15 (1.91)
46     17    927    782 ( 46.22)     0  0    0   0   0   0     0 (0.00)    0   15 (1.92)
45     52    979    765 ( 45.21)     0  0    0   0   0   0     0 (0.00)    0   15 (1.96)
44     26   1005    713 ( 42.14)     0  0    0   0   0   0     0 (0.00)    0   15 (2.10)
43     21   1026    687 ( 40.60)     0  0    0   0   0   0     0 (0.00)    0   15 (2.18)
42     64   1090    666 ( 39.36)     0  0    0   0   0   0     0 (0.00)    0   15 (2.25)
41      2   1092    602 ( 35.58)     0  0    0   0   0   0     0 (0.00)    0   15 (2.49)
40     51   1143    600 ( 35.46)     0  0    0   0   0   0     0 (0.00)    0   15 (2.50)
39      3   1146    549 ( 32.45)     0  0    0   0   0   0     0 (0.00)    0   15 (2.73)
38     10   1156    546 ( 32.27)     0  0    0   0   0   0     0 (0.00)    0   15 (2.75)
37     28   1184    536 ( 31.68)     0  0    0   0   0   0     0 (0.00)    0   15 (2.80)
36      9   1193    508 ( 30.02)     0  0    0   0   0   0     0 (0.00)    0   15 (2.95)
35     28   1221    499 ( 29.49)     0  0    0   0   0   0     0 (0.00)    0   15 (3.01)
34     10   1231    471 ( 27.84)     0  0    0   0   0   0     0 (0.00)    0   15 (3.18)
33     15   1246    461 ( 27.25)     0  0    0   0   0   0     0 (0.00)    0   15 (3.25)
32     10   1256    446 ( 26.36)     0  0    0   0   0   0     0 (0.00)    0   15 (3.36)
31      7   1263    436 ( 25.77)     0  0    0   0   0   0     0 (0.00)    0   15 (3.44)
30      8   1271    429 ( 25.35)     0  0    0   0   0   0     0 (0.00)    0   15 (3.50)
29     24   1295    421 ( 24.88)     0  0    0   0   0   0     0 (0.00)    0   15 (3.56)
28     16   1311    397 ( 23.46)     0  0    0   0   0   0     0 (0.00)    0   15 (3.78)
27     13   1324    381 ( 22.52)     0  0    0   0   0   0     0 (0.00)    0   15 (3.94)
26     23   1347    368 ( 21.75)     0  0    0   0   0   0     0 (0.00)    0   15 (4.08)
25     30   1377    345 ( 20.39)     0  0    0   0   0   0     0 (0.00)    0   15 (4.35)
24     24   1401    315 ( 18.62)     0  0    0   0   0   0     0 (0.00)    0   15 (4.76)
23     25   1426    291 ( 17.20)     0  0    0   0   0   0     0 (0.00)    0   15 (5.15)
22     15   1441    266 ( 15.72)     0  0    0   0   0   0     0 (0.00)    0   15 (5.64)
21     12   1453    251 ( 14.83)     0  0    0   0   0   0     0 (0.00)    0   15 (5.98)
20     25   1478    239 ( 14.13)     0  0    0   0   0   0     0 (0.00)    0   15 (6.28)
19     24   1502    214 ( 12.65)     0  0    0   0   0   1     1 (4.17)    1   15 (7.01)
18     13   1515    190 ( 11.23)     0  0    0   0   0   0     0 (0.00)    1   14 (7.37)
17      3   1518    177 ( 10.46)     0  0    0   0   0   0     0 (0.00)    1   14 (7.91)
16     12   1530    174 ( 10.28)     0  0    0   0   0   0     0 (0.00)    1   14 (8.05)
15     15   1545    162 (  9.57)     0  0    0   0   0   0     0 (0.00)    1   14 (8.64)
14     10   1555    147 (  8.69)     0  0    0   0   0   0     0 (0.00)    1   14 (9.52)
13     13   1568    137 (  8.10)     0  0    0   0   0   0     0 (0.00)    1   14 (10.22)
12      7   1575    124 (  7.33)     0  0    0   0   0   0     0 (0.00)    1   14 (11.29)
11     22   1597    117 (  6.91)     0  0    0   0   1   0     1 (4.55)    2   14 (11.97)
10     24   1621     95 (  5.61)     0  0    0   0   0   0     0 (0.00)    2   13 (13.68)
 9     28   1649     71 (  4.20)     0  0    0   0   1   2     3 (10.71)    5   13 (18.31)
 8     24   1673     43 (  2.54)     0  0    0   1   2   0     3 (12.50)    8   10 (23.26)
 7     11   1684     19 (  1.12)     0  0    0   2   2   0     4 (36.36)   12    7 (36.84)
 6      8   1692      8 (  0.47)     0  0    0   1   2   0     3 (37.50)   15    3 (37.50)
-1    231   1923      0 (  0.00)     2  0    0   7   7   0    14 (6.06)   29    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     163      163        2
  7       1      164        3
  8       3      167        4
  9       9      176        7
 10       3      179        7
 11       7      186        8
 12       2      188        8
 13       1      189        8
 14       7      196        9
 15       6      202       12
 16       3      205       12
 18       6      211       15
 19      15      226       19
 20      15      241       21
 21       5      246       22
 22      11      257       23
 23      18      275       25
 24      16      291       30
 25      21      312       33
 26      19      331       39
 27      11      342       36
 28      12      354       33
 29      18      372       28
 30       8      380       26
 31       6      386       26
 32      10      396       24
 33      15      411       28
 34      10      421       27
 35      28      449       24
 36       9      458       23
 37      28      486       27
 38      10      496       27
 39       3      499       26
 40      51      550       33
 41       2      552       34
 42      64      616       37
 43      21      637       43
 44      26      663       47
 45      52      715       55
 46      17      732       51
 47       2      734       51
 48      16      750       47
 49       1      751       46
 50      25      776       48
 51     229     1005       65
 56     637     1642        1

SS region: 1373 (83.62%), flagged: 1 (0.06%)

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):
*  698  D     aa090109f1      (63)/(54)  696 CGCC / CGC

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; 304 bp (untrimmed), 304 (trimmed).
C  -603   350 be120109r1    302 (  0)  0.00 0.00 0.00  604 (604)   46 ( 46) 
     -7   945 be120109f1    286 (  0)  1.32 0.33 0.00    8 (  8)  641 (641) 

Overall discrep rates (%):             0.66 0.16 0.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90     227  74.7     227  74.7    0.00
 89       2   0.7     229  75.3    0.00
 88       3   1.0     232  76.3    0.00
 86       5   1.6     237  78.0    0.00
 85       3   1.0     240  78.9    0.00
 84       4   1.3     244  80.3    0.00
 83       1   0.3     245  80.6    0.00
 82       1   0.3     246  80.9    0.00
 81       2   0.7     248  81.6    0.00
 80       1   0.3     249  81.9    0.00
 79       1   0.3     250  82.2    0.00
 78       1   0.3     251  82.6    0.00
 77       1   0.3     252  82.9    0.00
 75       2   0.7     254  83.6    0.00
 74       1   0.3     255  83.9    0.00
 71      14   4.6     269  88.5    0.00
 66       3   1.0     272  89.5    0.00
 64       2   0.7     274  90.1    0.00
 59       1   0.3     275  90.5    0.00
 58       2   0.7     277  91.1    0.00
 56      17   5.6     294  96.7    0.00
 51      10   3.3     304 100.0    0.00   (quality -1 = terminal quality 0)

Avg. full length: 304.0, trimmed (qual > -1): 304.0
Avg. quality: 84.6 per base

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

Regions of LLR- adjusted quality < 2.0:


1 regions, avg size 0.0, avg spacing 304.0

First_start: 1, last_end: 304

Slack, # used pairs (max_score), unused
 0     1  ( 6.1)     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+
  305 - right        0+      be120109f1   (  -7)    No            311+

Bottom strand: 
 left -     0        0+      be120109r1   ( 350)    Yes           350+
  305 - 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    280    280    609 (100.00)     0  0    0   0   0   0     0 (0.00)    0    5 (0.82)
51    145    425    329 ( 54.02)     0  0    0   0   0   0     0 (0.00)    0    5 (1.52)
48      7    432    184 ( 30.21)     0  0    0   0   0   0     0 (0.00)    0    5 (2.72)
47      2    434    177 ( 29.06)     0  0    0   0   0   0     0 (0.00)    0    5 (2.82)
46     13    447    175 ( 28.74)     0  0    0   0   0   0     0 (0.00)    0    5 (2.86)
45     24    471    162 ( 26.60)     0  0    0   0   0   0     0 (0.00)    0    5 (3.09)
44      3    474    138 ( 22.66)     0  0    0   0   0   0     0 (0.00)    0    5 (3.62)
43      4    478    135 ( 22.17)     0  0    0   0   0   0     0 (0.00)    0    5 (3.70)
42     13    491    131 ( 21.51)     0  0    0   0   0   0     0 (0.00)    0    5 (3.82)
40     28    519    118 ( 19.38)     0  0    0   0   0   0     0 (0.00)    0    5 (4.24)
39     12    531     90 ( 14.78)     0  0    0   0   0   0     0 (0.00)    0    5 (5.56)
38      2    533     78 ( 12.81)     0  0    0   0   0   0     0 (0.00)    0    5 (6.41)
37      2    535     76 ( 12.48)     0  0    0   0   0   0     0 (0.00)    0    5 (6.58)
36      2    537     74 ( 12.15)     0  0    0   0   0   0     0 (0.00)    0    5 (6.76)
35      5    542     72 ( 11.82)     0  0    0   0   0   0     0 (0.00)    0    5 (6.94)
34      6    548     67 ( 11.00)     0  0    0   0   0   0     0 (0.00)    0    5 (7.46)
32      6    554     61 ( 10.02)     0  0    0   0   0   0     0 (0.00)    0    5 (8.20)
29      6    560     55 (  9.03)     0  0    0   0   0   0     0 (0.00)    0    5 (9.09)
28      4    564     49 (  8.05)     0  0    0   0   0   0     0 (0.00)    0    5 (10.20)
27      1    565     45 (  7.39)     0  0    0   0   0   0     0 (0.00)    0    5 (11.11)
26      1    566     44 (  7.22)     0  0    0   0   0   0     0 (0.00)    0    5 (11.36)
25      4    570     43 (  7.06)     0  0    0   0   0   0     0 (0.00)    0    5 (11.63)
24      2    572     39 (  6.40)     0  0    0   0   0   0     0 (0.00)    0    5 (12.82)
23      1    573     37 (  6.08)     0  0    0   0   0   0     0 (0.00)    0    5 (13.51)
22      1    574     36 (  5.91)     0  0    0   0   0   0     0 (0.00)    0    5 (13.89)
21      2    576     35 (  5.75)     0  0    0   0   0   0     0 (0.00)    0    5 (14.29)
20      1    577     33 (  5.42)     0  0    0   0   0   0     0 (0.00)    0    5 (15.15)
19      3    580     32 (  5.25)     0  0    0   0   0   0     0 (0.00)    0    5 (15.62)
18      1    581     29 (  4.76)     0  0    0   0   0   0     0 (0.00)    0    5 (17.24)
15      2    583     28 (  4.60)     0  0    0   0   0   0     0 (0.00)    0    5 (17.86)
13      4    587     26 (  4.27)     0  0    0   0   0   0     0 (0.00)    0    5 (19.23)
12      0    587     22 (  3.61)     0  0    0   0   0   0     0 (0.00)    0    5 (22.73)
11      0    587     22 (  3.61)     0  0    0   0   0   0     0 (0.00)    0    5 (22.73)
10      0    587     22 (  3.61)     0  0    0   0   0   0     0 (0.00)    0    5 (22.73)
 9      4    591     22 (  3.61)     0  0    0   0   0   0     0 (0.00)    0    5 (22.73)
 8      5    596     18 (  2.96)     0  0    0   1   0   0     1 (20.00)    1    5 (27.78)
 7      5    601     13 (  2.13)     0  0    0   0   0   0     0 (0.00)    1    4 (30.77)
 6      5    606      8 (  1.31)     0  0    0   3   0   0     3 (60.00)    4    4 (50.00)
 4      2    608      3 (  0.49)     0  0    0   0   0   0     0 (0.00)    4    1 (33.33)
 0      1    609      1 (  0.16)     0  0    0   0   1   0     1 (100.00)    5    1 (100.00)
-1      0    609      0 (  0.00)     0  0    0   0   0   0     0 (0.00)    5    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    454    454    609 (100.00)     0  0    0   0   0   0     0 (0.00)    0    5 (0.82)
89      4    458    155 ( 25.45)     0  0    0   0   0   0     0 (0.00)    0    5 (3.23)
88      6    464    151 ( 24.79)     0  0    0   0   0   0     0 (0.00)    0    5 (3.31)
86     10    474    145 ( 23.81)     0  0    0   0   0   0     0 (0.00)    0    5 (3.45)
85      6    480    135 ( 22.17)     0  0    0   0   0   0     0 (0.00)    0    5 (3.70)
84      8    488    129 ( 21.18)     0  0    0   0   0   0     0 (0.00)    0    5 (3.88)
83      1    489    121 ( 19.87)     0  0    0   0   0   0     0 (0.00)    0    5 (4.13)
82      1    490    120 ( 19.70)     0  0    0   0   0   0     0 (0.00)    0    5 (4.17)
81      2    492    119 ( 19.54)     0  0    0   0   0   0     0 (0.00)    0    5 (4.20)
80      2    494    117 ( 19.21)     0  0    0   0   0   0     0 (0.00)    0    5 (4.27)
79      1    495    115 ( 18.88)     0  0    0   0   0   0     0 (0.00)    0    5 (4.35)
78      1    496    114 ( 18.72)     0  0    0   0   0   0     0 (0.00)    0    5 (4.39)
77      1    497    113 ( 18.56)     0  0    0   0   0   0     0 (0.00)    0    5 (4.42)
75      2    499    112 ( 18.39)     0  0    0   0   0   0     0 (0.00)    0    5 (4.46)
74      1    500    110 ( 18.06)     0  0    0   0   0   0     0 (0.00)    0    5 (4.55)
71     14    514    109 ( 17.90)     0  0    0   0   0   0     0 (0.00)    0    5 (4.59)
66      3    517     95 ( 15.60)     0  0    0   0   0   0     0 (0.00)    0    5 (5.26)
64      2    519     92 ( 15.11)     0  0    0   0   0   0     0 (0.00)    0    5 (5.43)
63      1    520     90 ( 14.78)     0  0    0   0   0   0     0 (0.00)    0    5 (5.56)
59      1    521     89 ( 14.61)     0  0    0   0   0   0     0 (0.00)    0    5 (5.62)
58      2    523     88 ( 14.45)     0  0    0   0   0   0     0 (0.00)    0    5 (5.68)
56     28    551     86 ( 14.12)     0  0    0   0   0   0     0 (0.00)    0    5 (5.81)
55      3    554     58 (  9.52)     0  0    0   0   0   0     0 (0.00)    0    5 (8.62)
51     15    569     55 (  9.03)     0  0    0   0   0   0     0 (0.00)    0    5 (9.09)
49      2    571     40 (  6.57)     0  0    0   0   0   0     0 (0.00)    0    5 (12.50)
47      2    573     38 (  6.24)     0  0    0   0   0   0     0 (0.00)    0    5 (13.16)
44      3    576     36 (  5.91)     0  0    0   0   0   0     0 (0.00)    0    5 (13.89)
42      1    577     33 (  5.42)     0  0    0   0   0   0     0 (0.00)    0    5 (15.15)
40      2    579     32 (  5.25)     0  0    0   0   0   0     0 (0.00)    0    5 (15.62)
39      1    580     30 (  4.93)     0  0    0   0   0   0     0 (0.00)    0    5 (16.67)
36      1    581     29 (  4.76)     0  0    0   0   0   0     0 (0.00)    0    5 (17.24)
35      1    582     28 (  4.60)     0  0    0   0   0   0     0 (0.00)    0    5 (17.86)
34      2    584     27 (  4.43)     0  0    0   0   0   0     0 (0.00)    0    5 (18.52)
28      1    585     25 (  4.11)     0  0    0   0   0   0     0 (0.00)    0    5 (20.00)
25      1    586     24 (  3.94)     0  0    0   0   0   0     0 (0.00)    0    5 (20.83)
24      1    587     23 (  3.78)     0  0    0   0   0   0     0 (0.00)    0    5 (21.74)
22      2    589     22 (  3.61)     0  0    0   0   0   0     0 (0.00)    0    5 (22.73)
15      2    591     20 (  3.28)     0  0    0   0   0   0     0 (0.00)    0    5 (25.00)
13      3    594     18 (  2.96)     0  0    0   0   0   0     0 (0.00)    0    5 (27.78)
 9      4    598     15 (  2.46)     0  0    0   0   0   0     0 (0.00)    0    5 (33.33)
 8      2    600     11 (  1.81)     0  0    0   1   0   0     1 (50.00)    1    5 (45.45)
 7      1    601      9 (  1.48)     0  0    0   0   0   0     0 (0.00)    1    4 (44.44)
 6      5    606      8 (  1.31)     0  0    0   3   0   0     3 (60.00)    4    4 (50.00)
 4      2    608      3 (  0.49)     0  0    0   0   0   0     0 (0.00)    4    1 (33.33)
 0      1    609      1 (  0.16)     0  0    0   0   1   0     1 (100.00)    5    1 (100.00)
-1      0    609      0 (  0.00)     0  0    0   0   0   0     0 (0.00)    5    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
 51      10       10        3
 56      17       27        5
 58       2       29        5
 59       1       30        5
 64       2       32        5
 66       3       35        5
 71      14       49        5
 74       1       50        6
 75       2       52        6
 77       1       53        6
 78       1       54        6
 79       1       55        5
 80       1       56        6
 81       2       58        7
 82       1       59        6
 83       1       60        5
 84       4       64        5
 85       3       67        6
 86       5       72        6
 88       3       75        6
 89       2       77        7
 90     227      304        1

SS region: 0 (0.00%), 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): 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 10.  2 reads; 980 bp (untrimmed), 703 (trimmed).  Isolated contig.
C     1   980 ag030109r1    910 (  0)  1.43 0.61 0.00    0 (190)    0 (210) 
     55  1045 ag030109f1    612 (  0)  3.38 0.95 0.54   51 (131)  200 (279) 

Overall discrep rates (%):             2.27 0.76 0.23

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90      28   2.9      28   2.9    0.00
 89       3   0.3      31   3.2    0.00
 88       6   0.6      37   3.8    0.00
 87       7   0.7      44   4.5    0.00
 86       2   0.2      46   4.7    0.00
 85      10   1.0      56   5.7    0.00
 84       8   0.8      64   6.5    0.00
 83      10   1.0      74   7.6    0.00
 82       4   0.4      78   8.0    0.00
 81       9   0.9      87   8.9    0.00
 80       6   0.6      93   9.5    0.00
 79      14   1.4     107  10.9    0.00
 78       5   0.5     112  11.4    0.00
 77      17   1.7     129  13.2    0.00
 76      10   1.0     139  14.2    0.00
 75       5   0.5     144  14.7    0.00
 74      15   1.5     159  16.2    0.00
 73       5   0.5     164  16.7    0.00
 72      10   1.0     174  17.8    0.00
 71      15   1.5     189  19.3    0.00
 70      10   1.0     199  20.3    0.00
 69      15   1.5     214  21.8    0.00
 68      21   2.1     235  24.0    0.00
 67      12   1.2     247  25.2    0.00
 66      10   1.0     257  26.2    0.00
 65      37   3.8     294  30.0    0.00
 64       9   0.9     303  30.9    0.00
 63      12   1.2     315  32.1    0.00
 62       7   0.7     322  32.9    0.00
 61      14   1.4     336  34.3    0.00
 60       7   0.7     343  35.0    0.00
 59      19   1.9     362  36.9    0.00
 58       8   0.8     370  37.8    0.00
 57      16   1.6     386  39.4    0.00
 56      92   9.4     478  48.8    0.00
 55       2   0.2     480  49.0    0.00
 54       6   0.6     486  49.6    0.00
 53       7   0.7     493  50.3    0.00
 52       5   0.5     498  50.8    0.00
 51      22   2.2     520  53.1    0.00
 50      20   2.0     540  55.1    0.00
 48       5   0.5     545  55.6    0.00
 47       5   0.5     550  56.1    0.00
 46      10   1.0     560  57.1    0.00
 45       2   0.2     562  57.3    0.00
 44      14   1.4     576  58.8    0.00
 43       4   0.4     580  59.2    0.00
 42      33   3.4     613  62.6    0.00
 41       1   0.1     614  62.7    0.00
 40      27   2.8     641  65.4    0.01
 37      19   1.9     660  67.3    0.01
 36       3   0.3     663  67.7    0.01
 35       3   0.3     666  68.0    0.01
 33       8   0.8     674  68.8    0.02
 31       1   0.1     675  68.9    0.02
 29       4   0.4     679  69.3    0.02
 28       2   0.2     681  69.5    0.03
 27       1   0.1     682  69.6    0.03
 26       2   0.2     684  69.8    0.03
 24       2   0.2     686  70.0    0.04
 21       2   0.2     688  70.2    0.06
 19       4   0.4     692  70.6    0.11
 16       3   0.3     695  70.9    0.18
 15       2   0.2     697  71.1    0.25
 14       1   0.1     698  71.2    0.29
 11       2   0.2     700  71.4    0.44
 10       2   0.2     702  71.6    0.64
  9       1   0.1     703  71.7    0.77
 -1     277  28.3     980 100.0  277.77   (quality -1 = terminal quality 0)

Avg. full length: 980.0, trimmed (qual > -1): 703.0
Avg. quality: 43.0 per base

Initial, terminal qual 0 segments:  1-187, 891-980

Regions of LLR- adjusted quality < 2.0:
1-188, 226-230, 857-863, 889-980, 

4 regions, avg size 73.0, avg spacing 245.0

First_start: 186, last_end: 770

Slack, # used pairs (max_score), unused
 0     0  ( 0.0)     0 ( 0.0)        1
 4     1  (15.4)     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 -   105      105+
  846 - right      135+      ag030109f1   (  55)    No            925+

Bottom strand: 
 left -     0        0+      ag030109r1   ( 980)    No            980+
  981 - 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    134    134   1534 (100.00)     0  0    0   0   0   0     0 (0.00)    0   55 (3.59)
51     26    160   1400 ( 91.26)     0  0    0   0   0   0     0 (0.00)    0   55 (3.93)
50    129    289   1374 ( 89.57)     0  0    0   0   0   0     0 (0.00)    0   55 (4.00)
48      3    292   1245 ( 81.16)     0  0    0   0   0   0     0 (0.00)    0   55 (4.42)
47     10    302   1242 ( 80.96)     0  0    0   0   0   0     0 (0.00)    0   55 (4.43)
46     18    320   1232 ( 80.31)     0  0    0   0   0   0     0 (0.00)    0   55 (4.46)
45      3    323   1214 ( 79.14)     0  0    0   0   0   0     0 (0.00)    0   55 (4.53)
44     74    397   1211 ( 78.94)     0  0    0   0   0   0     0 (0.00)    0   55 (4.54)
43     16    413   1137 ( 74.12)     0  0    0   0   0   0     0 (0.00)    0   55 (4.84)
42    139    552   1121 ( 73.08)     0  0    0   0   0   0     0 (0.00)    0   55 (4.91)
41     34    586    982 ( 64.02)     0  0    0   0   0   0     0 (0.00)    0   55 (5.60)
40     37    623    948 ( 61.80)     0  0    0   0   0   0     0 (0.00)    0   55 (5.80)
39      3    626    911 ( 59.39)     0  0    0   0   0   0     0 (0.00)    0   55 (6.04)
38      5    631    908 ( 59.19)     0  0    0   0   0   0     0 (0.00)    0   55 (6.06)
37     59    690    903 ( 58.87)     0  0    0   0   0   0     0 (0.00)    0   55 (6.09)
36     10    700    844 ( 55.02)     0  0    0   0   0   0     0 (0.00)    0   55 (6.52)
35     65    765    834 ( 54.37)     0  0    0   0   0   1     1 (1.54)    1   55 (6.59)
34      3    768    769 ( 50.13)     1  0    0   0   0   1     1 (33.33)    2   54 (7.02)
33     41    809    766 ( 49.93)     0  0    0   0   0   0     0 (0.00)    2   53 (6.92)
32     13    822    725 ( 47.26)     3  0    0   0   0   0     0 (0.00)    2   53 (7.31)
31      7    829    712 ( 46.41)     0  0    0   0   0   0     0 (0.00)    2   53 (7.44)
30     15    844    705 ( 45.96)     0  0    0   0   0   0     0 (0.00)    2   53 (7.52)
29     33    877    690 ( 44.98)     9  0    0   0   0   0     0 (0.00)    2   53 (7.68)
28     13    890    657 ( 42.83)     0  0    0   0   0   0     0 (0.00)    2   53 (8.07)
27     13    903    644 ( 41.98)     3  0    0   1   0   1     2 (15.38)    4   53 (8.23)
26     12    915    631 ( 41.13)     1  0    0   0   0   0     0 (0.00)    4   51 (8.08)
25      9    924    619 ( 40.35)     0  0    0   0   0   0     0 (0.00)    4   51 (8.24)
24     16    940    610 ( 39.77)     2  0    0   1   0   0     1 (6.25)    5   51 (8.36)
23     19    959    594 ( 38.72)     3  0    0   0   0   0     0 (0.00)    5   50 (8.42)
22     23    982    575 ( 37.48)     2  0    0   0   0   0     0 (0.00)    5   50 (8.70)
21     18   1000    552 ( 35.98)     0  0    0   1   0   0     1 (5.56)    6   50 (9.06)
20     15   1015    534 ( 34.81)     0  0    0   0   0   1     1 (6.67)    7   49 (9.18)
19     34   1049    519 ( 33.83)     1  0    0   0   1   0     1 (2.94)    8   48 (9.25)
18     23   1072    485 ( 31.62)     0  0    0   0   1   0     1 (4.35)    9   47 (9.69)
17     32   1104    462 ( 30.12)     1  0    0   0   2   0     2 (6.25)   11   46 (9.96)
16     20   1124    430 ( 28.03)     0  0    0   1   0   0     1 (5.00)   12   44 (10.23)
15     42   1166    410 ( 26.73)     0  0    0   2   0   0     2 (4.76)   14   43 (10.49)
14     29   1195    368 ( 23.99)     0  0    0   2   0   0     2 (6.90)   16   41 (11.14)
13     28   1223    339 ( 22.10)     1  0    0   0   1   0     1 (3.57)   17   39 (11.50)
12     25   1248    311 ( 20.27)     0  0    0   1   1   0     2 (8.00)   19   38 (12.22)
11     68   1316    286 ( 18.64)     0  0    0   4   0   0     4 (5.88)   23   36 (12.59)
10     70   1386    218 ( 14.21)     0  0    0   7   2   0     9 (12.86)   32   32 (14.68)
 9     77   1463    148 (  9.65)     0  0    0  11   2   0    13 (16.88)   45   23 (15.54)
 8     50   1513     71 (  4.63)     0  0    0   6   2   0     8 (16.00)   53   10 (14.08)
 7      4   1517     21 (  1.37)     0  0    0   1   0   0     1 (25.00)   54    2 (9.52)
 6     12   1529     17 (  1.11)     0  0    0   0   1   0     1 (8.33)   55    1 (5.88)
 4      5   1534      5 (  0.33)     0  0    0   0   0   0     0 (0.00)   55    0 (0.00)
-1    195   1729      0 (  0.00)   159  0    1   0   0   0     1 (0.51)   56    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     56     56   1291 (100.00)     0  0    0   0   0   0     0 (0.00)    0   17 (1.32)
89      6     62   1235 ( 95.66)     0  0    0   0   0   0     0 (0.00)    0   17 (1.38)
88     12     74   1229 ( 95.20)     0  0    0   0   0   0     0 (0.00)    0   17 (1.38)
87     14     88   1217 ( 94.27)     0  0    0   0   0   0     0 (0.00)    0   17 (1.40)
86      4     92   1203 ( 93.18)     0  0    0   0   0   0     0 (0.00)    0   17 (1.41)
85     20    112   1199 ( 92.87)     0  0    0   0   0   0     0 (0.00)    0   17 (1.42)
84     16    128   1179 ( 91.32)     0  0    0   0   0   0     0 (0.00)    0   17 (1.44)
83     20    148   1163 ( 90.09)     0  0    0   0   0   0     0 (0.00)    0   17 (1.46)
82      8    156   1143 ( 88.54)     0  0    0   0   0   0     0 (0.00)    0   17 (1.49)
81     18    174   1135 ( 87.92)     0  0    0   0   0   0     0 (0.00)    0   17 (1.50)
80     12    186   1117 ( 86.52)     0  0    0   0   0   0     0 (0.00)    0   17 (1.52)
79     28    214   1105 ( 85.59)     0  0    0   0   0   0     0 (0.00)    0   17 (1.54)
78     10    224   1077 ( 83.42)     0  0    0   0   0   0     0 (0.00)    0   17 (1.58)
77     34    258   1067 ( 82.65)     0  0    0   0   0   0     0 (0.00)    0   17 (1.59)
76     19    277   1033 ( 80.02)     0  0    0   0   0   0     0 (0.00)    0   17 (1.65)
75      9    286   1014 ( 78.54)     0  0    0   0   0   0     0 (0.00)    0   17 (1.68)
74     30    316   1005 ( 77.85)     0  0    0   0   0   0     0 (0.00)    0   17 (1.69)
73      8    324    975 ( 75.52)     0  0    0   0   0   0     0 (0.00)    0   17 (1.74)
72     20    344    967 ( 74.90)     0  0    0   0   0   0     0 (0.00)    0   17 (1.76)
71     25    369    947 ( 73.35)     0  0    0   0   0   0     0 (0.00)    0   17 (1.80)
70     19    388    922 ( 71.42)     0  0    0   0   0   0     0 (0.00)    0   17 (1.84)
69     29    417    903 ( 69.95)     0  0    0   0   0   0     0 (0.00)    0   17 (1.88)
68     40    457    874 ( 67.70)     0  0    0   0   0   0     0 (0.00)    0   17 (1.95)
67     22    479    834 ( 64.60)     0  0    0   0   0   0     0 (0.00)    0   17 (2.04)
66     16    495    812 ( 62.90)     0  0    0   0   0   0     0 (0.00)    0   17 (2.09)
65     53    548    796 ( 61.66)     0  0    0   0   0   0     0 (0.00)    0   17 (2.14)
64     16    564    743 ( 57.55)     0  0    0   0   0   0     0 (0.00)    0   17 (2.29)
63     23    587    727 ( 56.31)     0  0    0   0   0   0     0 (0.00)    0   17 (2.34)
62     12    599    704 ( 54.53)     0  0    0   0   0   0     0 (0.00)    0   17 (2.41)
61     29    628    692 ( 53.60)     0  0    0   0   0   0     0 (0.00)    0   17 (2.46)
60     14    642    663 ( 51.36)     0  0    0   0   0   0     0 (0.00)    0   17 (2.56)
59     28    670    649 ( 50.27)     0  0    0   0   0   0     0 (0.00)    0   17 (2.62)
58     10    680    621 ( 48.10)     0  0    0   0   0   0     0 (0.00)    0   17 (2.74)
57     25    705    611 ( 47.33)     0  0    0   0   0   0     0 (0.00)    0   17 (2.78)
56    110    815    586 ( 45.39)     0  0    0   0   0   0     0 (0.00)    0   17 (2.90)
55      8    823    476 ( 36.87)     0  0    0   0   0   0     0 (0.00)    0   17 (3.57)
54     11    834    468 ( 36.25)     0  0    0   0   0   0     0 (0.00)    0   17 (3.63)
53     15    849    457 ( 35.40)     0  0    0   0   0   0     0 (0.00)    0   17 (3.72)
52     11    860    442 ( 34.24)     0  0    0   0   0   0     0 (0.00)    0   17 (3.85)
51     29    889    431 ( 33.38)     0  0    0   0   0   0     0 (0.00)    0   17 (3.94)
50     28    917    402 ( 31.14)     0  0    0   0   0   0     0 (0.00)    0   17 (4.23)
48      6    923    374 ( 28.97)     0  0    0   0   0   0     0 (0.00)    0   17 (4.55)
47      7    930    368 ( 28.51)     0  0    0   0   0   0     0 (0.00)    0   17 (4.62)
46     11    941    361 ( 27.96)     0  0    0   0   0   0     0 (0.00)    0   17 (4.71)
45      2    943    350 ( 27.11)     0  0    0   0   0   0     0 (0.00)    0   17 (4.86)
44     23    966    348 ( 26.96)     0  0    0   0   0   0     0 (0.00)    0   17 (4.89)
43      6    972    325 ( 25.17)     0  0    0   0   0   0     0 (0.00)    0   17 (5.23)
42     49   1021    319 ( 24.71)     0  0    0   0   0   0     0 (0.00)    0   17 (5.33)
41      2   1023    270 ( 20.91)     0  0    0   0   0   0     0 (0.00)    0   17 (6.30)
40     32   1055    268 ( 20.76)     0  0    0   0   0   0     0 (0.00)    0   17 (6.34)
38      1   1056    236 ( 18.28)     0  0    0   0   0   0     0 (0.00)    0   17 (7.20)
37     23   1079    235 ( 18.20)     0  0    0   0   0   0     0 (0.00)    0   17 (7.23)
36      4   1083    212 ( 16.42)     0  0    0   0   0   0     0 (0.00)    0   17 (8.02)
35      3   1086    208 ( 16.11)     0  0    0   0   0   0     0 (0.00)    0   17 (8.17)
34      2   1088    205 ( 15.88)     0  0    0   0   0   0     0 (0.00)    0   17 (8.29)
33     11   1099    203 ( 15.72)     0  0    0   0   0   0     0 (0.00)    0   17 (8.37)
32     10   1109    192 ( 14.87)     0  0    0   0   0   0     0 (0.00)    0   17 (8.85)
31      7   1116    182 ( 14.10)     0  0    0   0   0   0     0 (0.00)    0   17 (9.34)
30      4   1120    175 ( 13.56)     0  0    0   0   0   0     0 (0.00)    0   17 (9.71)
29      9   1129    171 ( 13.25)     0  0    0   0   0   0     0 (0.00)    0   17 (9.94)
28      6   1135    162 ( 12.55)     0  0    0   0   0   0     0 (0.00)    0   17 (10.49)
27     11   1146    156 ( 12.08)     0  0    0   0   0   0     0 (0.00)    0   17 (10.90)
26      9   1155    145 ( 11.23)     0  0    0   0   0   0     0 (0.00)    0   17 (11.72)
25      3   1158    136 ( 10.53)     0  0    0   0   0   0     0 (0.00)    0   17 (12.50)
24     14   1172    133 ( 10.30)     0  0    0   0   0   0     0 (0.00)    0   17 (12.78)
23      4   1176    119 (  9.22)     0  0    0   0   0   0     0 (0.00)    0   17 (14.29)
22      5   1181    115 (  8.91)     0  0    0   0   0   0     0 (0.00)    0   17 (14.78)
21      3   1184    110 (  8.52)     0  0    0   0   0   0     0 (0.00)    0   17 (15.45)
20      2   1186    107 (  8.29)     0  0    0   0   0   0     0 (0.00)    0   17 (15.89)
19      7   1193    105 (  8.13)     0  0    0   0   0   0     0 (0.00)    0   17 (16.19)
18      5   1198     98 (  7.59)     0  0    0   0   1   0     1 (20.00)    1   17 (17.35)
17      7   1205     93 (  7.20)     0  0    0   0   1   0     1 (14.29)    2   16 (17.20)
16      5   1210     86 (  6.66)     0  0    0   0   0   0     0 (0.00)    2   15 (17.44)
15      9   1219     81 (  6.27)     0  0    0   2   0   0     2 (22.22)    4   15 (18.52)
14      8   1227     72 (  5.58)     0  0    0   1   0   0     1 (12.50)    5   13 (18.06)
13      8   1235     64 (  4.96)     0  0    0   0   1   0     1 (12.50)    6   12 (18.75)
12      6   1241     56 (  4.34)     0  0    0   1   1   0     2 (33.33)    8   11 (19.64)
11      5   1246     50 (  3.87)     0  0    0   0   0   0     0 (0.00)    8    9 (18.00)
10     17   1263     45 (  3.49)     0  0    0   2   1   0     3 (17.65)   11    9 (20.00)
 9     16   1279     28 (  2.17)     0  0    0   3   1   0     4 (25.00)   15    6 (21.43)
 8      7   1286     12 (  0.93)     0  0    0   1   0   0     1 (14.29)   16    2 (16.67)
 7      4   1290      5 (  0.39)     0  0    0   1   0   0     1 (25.00)   17    1 (20.00)
 6      1   1291      1 (  0.08)     0  0    0   0   0   0     0 (0.00)   17    0 (0.00)
-1    438   1729      0 (  0.00)   186  0    1  27   7   4    39 (8.90)   56    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     277      277        2
  9       1      278        3
 10       2      280        3
 11       2      282        3
 14       1      283        3
 15       2      285        4
 16       3      288        4
 19       4      292        4
 21       2      294        4
 24       2      296        4
 26       2      298        5
 27       1      299        5
 28       2      301        4
 29       4      305        5
 31       1      306        5
 33       8      314        6
 35       3      317        8
 36       3      320        8
 37      19      339       12
 40      27      366       15
 41       1      367       16
 42      33      400       24
 43       4      404       24
 44      14      418       21
 45       2      420       22
 46      10      430       22
 47       5      435       21
 48       5      440       22
 50      20      460       26
 51      22      482       26
 52       5      487       26
 53       7      494       26
 54       6      500       29
 55       2      502       30
 56      92      594       24
 57      16      610       30
 58       8      618       33
 59      19      637       37
 60       7      644       36
 61      14      658       39
 62       7      665       41
 63      12      677       45
 64       9      686       45
 65      37      723       42
 66      10      733       41
 67      12      745       38
 68      21      766       38
 69      15      781       39
 70      10      791       37
 71      15      806       30
 72      10      816       31
 73       5      821       29
 74      15      836       30
 75       5      841       27
 76      10      851       24
 77      17      868       23
 78       5      873       22
 79      14      887       23
 80       6      893       23
 81       9      902       22
 82       4      906       21
 83      10      916       21
 84       8      924       19
 85      10      934       17
 86       2      936       16
 87       7      943       18
 88       6      949       18
 89       3      952       16
 90      28      980        1

SS region: 240 (24.49%), 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):
  121     -3.5  [-3.5,  0.0]  (1, 0)
  156     -3.4  [-3.4,  0.0]  (1, 0)

Read/contig discrepancies (* = higher-quality):
   170  S   C ag030109r1      (0)/(0)  166 GTGAAC / GGGACC
   179  I   C ag030109r1      (0)/(0)  173 ATTCCTAT / AGGCTAAAT
   917  S   C ag030109r1      (0)/(0)  916 TNA / TNA
   115  S     ag030109f1      (0)/(0)  111 TTAGAT / TTGTT
   121  D     ag030109f1      (0)/(0)  119 GGGC / GGC
   130  D     ag030109f1      (0)/(0)  127 AAGGA / ATGA
   142  S     ag030109f1      (0)/(0)  138 CGCCCT / CCCTTT
   149  I     ag030109f1      (0)/(0)  147 ACCA / AGGGA
   156  D     ag030109f1      (0)/(0)  154 GAGC / GAC

0 HQ discrepancies in 0 reads.
9 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.  3 reads; 49 bp (untrimmed), 0 (trimmed).  Isolated contig.
      1   988 bd100109r1     46 (  0)  0.00 0.00 0.00    0 (  9)  939 (939) 
      2   946 af110109r1     31 (  0)  5.00 0.00 0.00    8 (  8)  897 (897) 
      3   959 be110109r1     29 (  0)  3.03 0.00 0.00   14 ( 15)  910 (910) 

Overall discrep rates (%):             2.46 0.00 0.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 -1      49 100.0      49 100.0   49.00   (quality -1 = terminal quality 0)

Avg. full length: 49.0, trimmed (qual > -1): 0.0
Avg. quality: 0.0 per base

Initial, terminal qual 0 segments:  1-49, (None)

Regions of LLR- adjusted quality < 2.0:
1-49, 

1 regions, avg size 49.0, avg spacing 49.0

First_start: 10, last_end: 49

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+
   50 - right        0+      be110109r1   (   3)    No             46+

Bottom strand: 
 left - right       49+

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    112 (100.00)     0  0    0   0   0   0     0 (0.00)    0    3 (2.68)
46      1      3    110 ( 98.21)     0  0    0   0   0   0     0 (0.00)    0    3 (2.73)
40      5      8    109 ( 97.32)     0  0    0   0   0   0     0 (0.00)    0    3 (2.75)
37      2     10    104 ( 92.86)     0  0    0   0   0   0     0 (0.00)    0    3 (2.88)
34      1     11    102 ( 91.07)     0  0    0   0   0   0     0 (0.00)    0    3 (2.94)
32      3     14    101 ( 90.18)     0  0    0   0   0   0     0 (0.00)    0    3 (2.97)
29      6     20     98 ( 87.50)     0  0    0   0   0   0     0 (0.00)    0    3 (3.06)
27      4     24     92 ( 82.14)     0  0    0   0   0   0     0 (0.00)    0    3 (3.26)
26      1     25     88 ( 78.57)     0  0    0   0   0   0     0 (0.00)    0    3 (3.41)
25      6     31     87 ( 77.68)     0  0    0   0   0   0     0 (0.00)    0    3 (3.45)
24      7     38     81 ( 72.32)     0  0    0   0   0   0     0 (0.00)    0    3 (3.70)
23      4     42     74 ( 66.07)     0  0    0   0   0   0     0 (0.00)    0    3 (4.05)
22      3     45     70 ( 62.50)     0  0    0   0   0   0     0 (0.00)    0    3 (4.29)
21      7     52     67 ( 59.82)     0  0    0   0   0   0     0 (0.00)    0    3 (4.48)
20      3     55     60 ( 53.57)     0  0    0   0   0   0     0 (0.00)    0    3 (5.00)
19      4     59     57 ( 50.89)     0  0    0   1   0   0     1 (25.00)    1    3 (5.26)
18      3     62     53 ( 47.32)     0  0    0   0   0   0     0 (0.00)    1    2 (3.77)
17      4     66     50 ( 44.64)     0  0    0   0   0   0     0 (0.00)    1    2 (4.00)
16      1     67     46 ( 41.07)     0  0    0   0   0   0     0 (0.00)    1    2 (4.35)
15      3     70     45 ( 40.18)     0  0    0   1   0   0     1 (33.33)    2    2 (4.44)
12      1     71     42 ( 37.50)     0  0    0   1   0   0     1 (100.00)    3    1 (2.38)
11      5     76     41 ( 36.61)     0  0    0   0   0   0     0 (0.00)    3    0 (0.00)
10      4     80     36 ( 32.14)     0  0    0   0   0   0     0 (0.00)    3    0 (0.00)
 9     11     91     32 ( 28.57)     0  0    0   0   0   0     0 (0.00)    3    0 (0.00)
 8      7     98     21 ( 18.75)     0  0    0   0   0   0     0 (0.00)    3    0 (0.00)
 7      7    105     14 ( 12.50)     0  0    0   0   0   0     0 (0.00)    3    0 (0.00)
 6      7    112      7 (  6.25)     0  0    0   0   0   0     0 (0.00)    3    0 (0.00)
-1     10    122      0 (  0.00)    22  0    0   0   0   0     0 (0.00)    3    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    122    122      0 (  0.00)    22  0    0   3   0   0     3 (2.46)    3    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      49       49        1

SS region: 49 (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):
    17  S     af110109r1      (0)/(0)  16 CTG / CGG
    26  S     af110109r1      (0)/(0)  25 GGC / GCC
    26  S     be110109r1      (0)/(0)  25 GGC / GCC

0 HQ discrepancies in 0 reads.
3 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; 1513 bp (untrimmed), 1428 (trimmed).  Isolated contig.
    -48   924 ab020109r1    806 (  0)  2.54 0.88 0.22   49 ( 49)   17 ( 17) 
    -42   929 bb010109r1    701 (  0)  2.47 1.48 0.00   43 ( 43)  119 (174) 
C   544  1513 bb010109f1    888 (  0)  1.24 0.21 0.72    0 ( 22)    0 (606) 

Overall discrep rates (%):             2.05 0.82 0.33

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 66     264  17.4     264  17.4    0.00
 64       2   0.1     266  17.6    0.00
 63       2   0.1     268  17.7    0.00
 62       1   0.1     269  17.8    0.00
 61      35   2.3     304  20.1    0.00
 60      45   3.0     349  23.1    0.00
 59       1   0.1     350  23.1    0.00
 58       8   0.5     358  23.7    0.00
 57       4   0.3     362  23.9    0.00
 56      32   2.1     394  26.0    0.00
 55      21   1.4     415  27.4    0.00
 54      15   1.0     430  28.4    0.00
 53       9   0.6     439  29.0    0.00
 52      21   1.4     460  30.4    0.00
 51      19   1.3     479  31.7    0.00
 50      44   2.9     523  34.6    0.00
 49       1   0.1     524  34.6    0.00
 48       5   0.3     529  35.0    0.00
 47       9   0.6     538  35.6    0.00
 46      10   0.7     548  36.2    0.00
 45       9   0.6     557  36.8    0.00
 44      37   2.4     594  39.3    0.00
 43      13   0.9     607  40.1    0.00
 42      49   3.2     656  43.4    0.01
 41      22   1.5     678  44.8    0.01
 40      23   1.5     701  46.3    0.01
 39      16   1.1     717  47.4    0.01
 38       7   0.5     724  47.9    0.01
 37     119   7.9     843  55.7    0.04
 36      15   1.0     858  56.7    0.04
 35     104   6.9     962  63.6    0.07
 34      20   1.3     982  64.9    0.08
 33      81   5.4    1063  70.3    0.12
 32      14   0.9    1077  71.2    0.13
 31      26   1.7    1103  72.9    0.15
 30      36   2.4    1139  75.3    0.19
 29      33   2.2    1172  77.5    0.23
 28      41   2.7    1213  80.2    0.30
 27      26   1.7    1239  81.9    0.35
 26      18   1.2    1257  83.1    0.39
 25      19   1.3    1276  84.3    0.45
 24      30   2.0    1306  86.3    0.57
 23      12   0.8    1318  87.1    0.63
 22      15   1.0    1333  88.1    0.73
 21      23   1.5    1356  89.6    0.91
 20       3   0.2    1359  89.8    0.94
 19       7   0.5    1366  90.3    1.03
 18       7   0.5    1373  90.7    1.14
 17      10   0.7    1383  91.4    1.34
 16       9   0.6    1392  92.0    1.56
 15       7   0.5    1399  92.5    1.79
 14       2   0.1    1401  92.6    1.87
 13       8   0.5    1409  93.1    2.27
 12       3   0.2    1412  93.3    2.46
 11       7   0.5    1419  93.8    3.01
 10       1   0.1    1420  93.9    3.11
  9       4   0.3    1424  94.1    3.61
  8       1   0.1    1425  94.2    3.77
  7       3   0.2    1428  94.4    4.37
 -1      85   5.6    1513 100.0   89.37   (quality -1 = terminal quality 0)

Avg. full length: 1513.0, trimmed (qual > -1): 1428.0
Avg. quality: 40.5 per base

Initial, terminal qual 0 segments:  (None), 1429-1513

Regions of LLR- adjusted quality < 2.0:
30-35, 67-71, 636, 663, 674-679, 763-765, 776-783, 822-823, 
851, 854, 856-862, 873-875, 893-895, 897-899, 1103, 1111, 
1276-1279, 1304-1307, 1393-1399, 1427-1513, 

20 regions, avg size 7.7, avg spacing 75.7

First_start: 1, last_end: 907

Slack, # used pairs (max_score), unused
 0     0  ( 0.0)     0 ( 0.0)        1
 1     1  ( 7.4)     0 ( 0.0)        2
 3     1  (15.0)     0 ( 0.0)        0
 5     1  ( 4.9)     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+
  908 - right      606+      bb010109r1   ( -42)    No           1555+

Bottom strand: 
 left -   543      543+      bb010109f1   (1513)    No           1513+
 1514 - 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    288    288   2682 (100.00)     0  0    0   0   0   0     0 (0.00)    0   86 (3.21)
51     45    333   2394 ( 89.26)     0  0    0   0   0   0     0 (0.00)    0   86 (3.59)
50     56    389   2349 ( 87.58)     0  0    0   0   0   0     0 (0.00)    0   86 (3.66)
48     15    404   2293 ( 85.50)     0  0    0   0   0   0     0 (0.00)    0   86 (3.75)
47      3    407   2278 ( 84.94)     0  0    0   0   0   0     0 (0.00)    0   86 (3.78)
46     14    421   2275 ( 84.82)     0  0    0   0   0   0     0 (0.00)    0   86 (3.78)
45     21    442   2261 ( 84.30)     0  0    0   0   0   0     0 (0.00)    0   86 (3.80)
44     43    485   2240 ( 83.52)     0  0    0   0   0   0     0 (0.00)    0   86 (3.84)
43      9    494   2197 ( 81.92)     0  0    0   0   0   0     0 (0.00)    0   86 (3.91)
42     70    564   2188 ( 81.58)     0  0    0   0   0   0     0 (0.00)    0   86 (3.93)
41     24    588   2118 ( 78.97)     0  0    0   0   0   0     0 (0.00)    0   86 (4.06)
40     46    634   2094 ( 78.08)     0  0    0   0   0   0     0 (0.00)    0   86 (4.11)
39     13    647   2048 ( 76.36)     0  0    0   0   0   0     0 (0.00)    0   86 (4.20)
37    152    799   2035 ( 75.88)     0  0    0   0   0   0     0 (0.00)    0   86 (4.23)
36      4    803   1883 ( 70.21)     0  0    0   0   0   0     0 (0.00)    0   86 (4.57)
35    131    934   1879 ( 70.06)     0  0    0   0   0   0     0 (0.00)    0   86 (4.58)
34     26    960   1748 ( 65.18)     0  0    0   0   0   0     0 (0.00)    0   86 (4.92)
33    137   1097   1722 ( 64.21)     0  0    0   0   0   0     0 (0.00)    0   86 (4.99)
32     16   1113   1585 ( 59.10)     0  0    0   0   0   0     0 (0.00)    0   86 (5.43)
31     48   1161   1569 ( 58.50)     0  0    0   0   0   0     0 (0.00)    0   86 (5.48)
30     77   1238   1521 ( 56.71)     0  0    0   0   0   0     0 (0.00)    0   86 (5.65)
29     91   1329   1444 ( 53.84)     0  0    0   0   0   0     0 (0.00)    0   86 (5.96)
28     58   1387   1353 ( 50.45)     0  0    0   0   0   0     0 (0.00)    0   86 (6.36)
27     70   1457   1295 ( 48.28)     0  0    0   0   0   0     0 (0.00)    0   86 (6.64)
26     33   1490   1225 ( 45.67)     0  0    0   0   0   0     0 (0.00)    0   86 (7.02)
25     43   1533   1192 ( 44.44)     0  0    0   0   0   1     1 (2.33)    1   86 (7.21)
24     82   1615   1149 ( 42.84)     0  0    0   0   0   0     0 (0.00)    1   85 (7.40)
23     51   1666   1067 ( 39.78)     0  0    0   0   0   0     0 (0.00)    1   85 (7.97)
22     64   1730   1016 ( 37.88)     0  0    0   0   0   2     2 (3.12)    3   85 (8.37)
21     78   1808    952 ( 35.50)     0  0    0   1   0   0     1 (1.28)    4   83 (8.72)
20     43   1851    874 ( 32.59)     0  0    0   0   0   1     1 (2.33)    5   82 (9.38)
19     54   1905    831 ( 30.98)     0  0    0   0   0   1     1 (1.85)    6   81 (9.75)
18     42   1947    777 ( 28.97)     0  0    0   1   0   0     1 (2.38)    7   80 (10.30)
17     47   1994    735 ( 27.40)     0  0    0   0   2   0     2 (4.26)    9   79 (10.75)
16     51   2045    688 ( 25.65)     0  0    0   3   2   0     5 (9.80)   14   77 (11.19)
15     33   2078    637 ( 23.75)     0  0    0   0   0   0     0 (0.00)   14   72 (11.30)
14     37   2115    604 ( 22.52)     0  0    0   0   1   0     1 (2.70)   15   72 (11.92)
13     66   2181    567 ( 21.14)     0  0    0   2   0   0     2 (3.03)   17   71 (12.52)
12     47   2228    501 ( 18.68)     0  0    0   2   1   0     3 (6.38)   20   69 (13.77)
11     96   2324    454 ( 16.93)     0  0    0   6   3   1    10 (10.42)   30   66 (14.54)
10     88   2412    358 ( 13.35)     0  0    0   5   3   0     8 (9.09)   38   56 (15.64)
 9    116   2528    270 ( 10.07)     0  0    0  10   2   1    13 (11.21)   51   48 (17.78)
 8     57   2585    154 (  5.74)     0  0    0   8   1   1    10 (17.54)   61   35 (22.73)
 7     51   2636     97 (  3.62)     0  0    0   6   3   1    10 (19.61)   71   25 (25.77)
 6     22   2658     46 (  1.72)     0  0    0   3   4   0     7 (31.82)   78   15 (32.61)
 4     18   2676     24 (  0.89)     0  0    0   2   0   0     2 (11.11)   80    8 (33.33)
 0      6   2682      6 (  0.22)     0  0    6   0   0   0     6 (100.00)   86    6 (100.00)
-1     18   2700      0 (  0.00)   136  0    0   0   0   0     0 (0.00)   86    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    502    502   2538 (100.00)     0  0    0   0   0   0     0 (0.00)    0   66 (2.60)
64      3    505   2036 ( 80.22)     0  0    0   0   0   0     0 (0.00)    0   66 (3.24)
63      2    507   2033 ( 80.10)     0  0    0   0   0   0     0 (0.00)    0   66 (3.25)
62      2    509   2031 ( 80.02)     0  0    0   0   0   0     0 (0.00)    0   66 (3.25)
61     62    571   2029 ( 79.94)     0  0    0   0   0   0     0 (0.00)    0   66 (3.25)
60     85    656   1967 ( 77.50)     0  0    0   0   0   0     0 (0.00)    0   66 (3.36)
59      2    658   1882 ( 74.15)     0  0    0   0   0   0     0 (0.00)    0   66 (3.51)
58     15    673   1880 ( 74.07)     0  0    0   0   0   0     0 (0.00)    0   66 (3.51)
57      6    679   1865 ( 73.48)     0  0    0   0   0   0     0 (0.00)    0   66 (3.54)
56     50    729   1859 ( 73.25)     0  0    0   0   0   0     0 (0.00)    0   66 (3.55)
55     35    764   1809 ( 71.28)     0  0    0   0   0   0     0 (0.00)    0   66 (3.65)
54     29    793   1774 ( 69.90)     0  0    0   0   0   0     0 (0.00)    0   66 (3.72)
53     13    806   1745 ( 68.75)     0  0    0   0   0   0     0 (0.00)    0   66 (3.78)
52     41    847   1732 ( 68.24)     0  0    0   0   0   0     0 (0.00)    0   66 (3.81)
51     28    875   1691 ( 66.63)     0  0    0   0   0   0     0 (0.00)    0   66 (3.90)
50     75    950   1663 ( 65.52)     0  0    0   0   0   0     0 (0.00)    0   66 (3.97)
49      1    951   1588 ( 62.57)     0  0    0   0   0   0     0 (0.00)    0   66 (4.16)
48      5    956   1587 ( 62.53)     0  0    0   0   0   0     0 (0.00)    0   66 (4.16)
47     13    969   1582 ( 62.33)     0  0    0   0   0   0     0 (0.00)    0   66 (4.17)
46     12    981   1569 ( 61.82)     0  0    0   0   0   0     0 (0.00)    0   66 (4.21)
45     20   1001   1557 ( 61.35)     0  0    0   0   0   0     0 (0.00)    0   66 (4.24)
44     41   1042   1537 ( 60.56)     0  0    0   0   0   0     0 (0.00)    0   66 (4.29)
43     23   1065   1496 ( 58.94)     0  0    0   0   0   0     0 (0.00)    0   66 (4.41)
42     53   1118   1473 ( 58.04)     0  0    0   0   0   0     0 (0.00)    0   66 (4.48)
41     25   1143   1420 ( 55.95)     0  0    0   0   0   0     0 (0.00)    0   66 (4.65)
40     36   1179   1395 ( 54.96)     0  0    0   0   0   0     0 (0.00)    0   66 (4.73)
39     18   1197   1359 ( 53.55)     0  0    0   0   0   0     0 (0.00)    0   66 (4.86)
38     13   1210   1341 ( 52.84)     0  0    0   0   0   0     0 (0.00)    0   66 (4.92)
37    126   1336   1328 ( 52.32)     0  0    0   0   0   0     0 (0.00)    0   66 (4.97)
36     18   1354   1202 ( 47.36)     0  0    0   0   0   1     1 (5.56)    1   66 (5.49)
35    122   1476   1184 ( 46.65)     0  0    0   0   0   0     0 (0.00)    1   65 (5.49)
34     33   1509   1062 ( 41.84)     0  0    0   0   0   0     0 (0.00)    1   65 (6.12)
33     93   1602   1029 ( 40.54)     0  0    0   0   0   0     0 (0.00)    1   65 (6.32)
32     19   1621    936 ( 36.88)     0  0    0   0   0   0     0 (0.00)    1   65 (6.94)
31     33   1654    917 ( 36.13)     0  0    0   0   0   0     0 (0.00)    1   65 (7.09)
30     49   1703    884 ( 34.83)     0  0    0   0   0   0     0 (0.00)    1   65 (7.35)
29     58   1761    835 ( 32.90)     0  0    0   0   0   0     0 (0.00)    1   65 (7.78)
28     53   1814    777 ( 30.61)     0  0    0   0   0   0     0 (0.00)    1   65 (8.37)
27     41   1855    724 ( 28.53)     0  0    0   0   0   0     0 (0.00)    1   65 (8.98)
26     28   1883    683 ( 26.91)     0  0    0   0   0   0     0 (0.00)    1   65 (9.52)
25     55   1938    655 ( 25.81)     0  0    0   0   0   1     1 (1.82)    2   65 (9.92)
24     62   2000    600 ( 23.64)     0  0    0   0   0   0     0 (0.00)    2   64 (10.67)
23     39   2039    538 ( 21.20)     0  0    0   0   0   0     0 (0.00)    2   64 (11.90)
22     25   2064    499 ( 19.66)     0  0    0   0   0   2     2 (8.00)    4   64 (12.83)
21     35   2099    474 ( 18.68)     0  0    0   1   0   0     1 (2.86)    5   62 (13.08)
20     19   2118    439 ( 17.30)     0  0    0   0   0   1     1 (5.26)    6   61 (13.90)
19     28   2146    420 ( 16.55)     0  0    0   0   0   1     1 (3.57)    7   60 (14.29)
18     16   2162    392 ( 15.45)     0  0    0   1   0   0     1 (6.25)    8   59 (15.05)
17     20   2182    376 ( 14.81)     0  0    0   0   2   0     2 (10.00)   10   58 (15.43)
16     28   2210    356 ( 14.03)     0  0    0   1   1   0     2 (7.14)   12   56 (15.73)
15     25   2235    328 ( 12.92)     0  0    0   0   0   0     0 (0.00)   12   54 (16.46)
14     14   2249    303 ( 11.94)     0  0    0   0   1   0     1 (7.14)   13   54 (17.82)
13     33   2282    289 ( 11.39)     0  0    0   2   0   0     2 (6.06)   15   53 (18.34)
12     20   2302    256 ( 10.09)     0  0    0   2   1   0     3 (15.00)   18   51 (19.92)
11     56   2358    236 (  9.30)     0  0    0   5   3   0     8 (14.29)   26   48 (20.34)
10     41   2399    180 (  7.09)     0  0    0   3   2   0     5 (12.20)   31   40 (22.22)
 9     44   2443    139 (  5.48)     0  0    0   4   1   1     6 (13.64)   37   35 (25.18)
 8     29   2472     95 (  3.74)     0  0    0   6   1   1     8 (27.59)   45   29 (30.53)
 7     27   2499     66 (  2.60)     0  0    0   3   3   1     7 (25.93)   52   21 (31.82)
 6     15   2514     39 (  1.54)     0  0    0   3   3   0     6 (40.00)   58   14 (35.90)
 4     18   2532     24 (  0.95)     0  0    0   2   0   0     2 (11.11)   60    8 (33.33)
 0      6   2538      6 (  0.24)     0  0    6   0   0   0     6 (100.00)   66    6 (100.00)
-1    162   2700      0 (  0.00)   136  0    0  16   4   0    20 (12.35)   86    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      85       85        1
  7       3       88        3
  8       1       89        3
  9       4       93        4
 10       1       94        5
 11       7      101        8
 12       3      104       10
 13       8      112       13
 14       2      114       12
 15       7      121       12
 16       9      130       14
 17      10      140       18
 18       7      147       19
 19       7      154       20
 20       3      157       21
 21      23      180       27
 22      15      195       31
 23      12      207       34
 24      30      237       44
 25      19      256       44
 26      18      274       45
 27      26      300       53
 28      41      341       50
 29      33      374       60
 30      36      410       65
 31      26      436       65
 32      14      450       71
 33      81      531       64
 34      20      551       61
 35     104      655       69
 36      15      670       64
 37     119      789       62
 38       7      796       61
 39      16      812       59
 40      23      835       59
 41      22      857       58
 42      49      906       40
 43      13      919       39
 44      37      956       32
 45       9      965       33
 46      10      975       29
 47       9      984       27
 48       5      989       24
 49       1      990       23
 50      44     1034       23
 51      19     1053       28
 52      21     1074       27
 53       9     1083       28
 54      15     1098       33
 55      21     1119       30
 56      32     1151       30
 57       4     1155       31
 58       8     1163       30
 59       1     1164       31
 60      45     1209       32
 61      35     1244       32
 62       1     1245       31
 63       2     1247       31
 64       2     1249       29
 66     264     1513        1

SS region: 1149 (75.94%), flagged: 1 (0.07%)

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):
*  855  D   C bb010109f1      (74)/(59)  853 CCCT / CCT
*  873  D   C bb010109f1      (65)/(64)  871 CGCC / CGC
*  898  D   C bb010109f1      (125)/(136)  892 GCCGTGGC / GCGTGC

3 HQ discrepancies in 1 reads.
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 13.  4 reads; 49 bp (untrimmed), 0 (trimmed).  Isolated contig.
      1   979 bb100109r1     44 (  0)  0.00 0.00 0.00    0 ( 18)  930 (930) 
      1   977 ae050109r1     30 (  0)  4.55 0.00 2.27    5 ( 16)  928 (928) 
      3   951 bg120109r1     30 (  0)  0.00 0.00 0.00   16 ( 13)  902 (902) 
      1   976 bg070109r1     29 (  0)  0.00 0.00 4.76    7 ( 13)  927 (927) 

Overall discrep rates (%):             1.20 0.00 1.81

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 -1      49 100.0      49 100.0   49.00   (quality -1 = terminal quality 0)

Avg. full length: 49.0, trimmed (qual > -1): 0.0
Avg. quality: 0.0 per base

Initial, terminal qual 0 segments:  1-49, (None)

Regions of LLR- adjusted quality < 2.0:
1-49, 

1 regions, avg size 49.0, avg spacing 49.0

First_start: 16, last_end: 49

Slack, # used pairs (max_score), unused
 0     5  ( 0.0)     0 ( 0.0)        5

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
   50 - right        0+      bg120109r1   (   3)    No             46+

Bottom strand: 
 left - right       49+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
48     13     13    158 (100.00)     0  0    0   0   0   0     0 (0.00)    0    5 (3.16)
44      1     14    145 ( 91.77)     0  0    0   0   0   0     0 (0.00)    0    5 (3.45)
40     11     25    144 ( 91.14)     0  0    0   0   0   0     0 (0.00)    0    5 (3.47)
32      5     30    133 ( 84.18)     0  0    0   0   0   0     0 (0.00)    0    5 (3.76)
31      1     31    128 ( 81.01)     0  0    0   0   0   0     0 (0.00)    0    5 (3.91)
29      2     33    127 ( 80.38)     0  0    0   0   0   0     0 (0.00)    0    5 (3.94)
27      4     37    125 ( 79.11)     0  0    0   0   0   0     0 (0.00)    0    5 (4.00)
26      2     39    121 ( 76.58)     0  0    0   0   0   0     0 (0.00)    0    5 (4.13)
25     10     49    119 ( 75.32)     0  0    0   0   0   0     0 (0.00)    0    5 (4.20)
24      2     51    109 ( 68.99)     0  0    0   0   0   0     0 (0.00)    0    5 (4.59)
23      7     58    107 ( 67.72)     0  0    0   0   0   0     0 (0.00)    0    5 (4.67)
22      4     62    100 ( 63.29)     0  0    0   0   0   0     0 (0.00)    0    5 (5.00)
20      3     65     96 ( 60.76)     0  0    0   0   0   0     0 (0.00)    0    5 (5.21)
19      1     66     93 ( 58.86)     0  0    0   0   0   0     0 (0.00)    0    5 (5.38)
18      7     73     92 ( 58.23)     0  0    0   0   0   0     0 (0.00)    0    5 (5.43)
17      7     80     85 ( 53.80)     0  0    0   0   0   0     0 (0.00)    0    5 (5.88)
16      3     83     78 ( 49.37)     0  0    0   0   0   0     0 (0.00)    0    5 (6.41)
15      5     88     75 ( 47.47)     0  0    0   0   0   0     0 (0.00)    0    5 (6.67)
13      8     96     70 ( 44.30)     0  0    0   0   0   1     1 (12.50)    1    5 (7.14)
12     10    106     62 ( 39.24)     0  0    0   0   0   0     0 (0.00)    1    4 (6.45)
11      6    112     52 ( 32.91)     0  0    0   0   0   0     0 (0.00)    1    4 (7.69)
10     14    126     46 ( 29.11)     1  0    0   1   0   0     1 (7.14)    2    4 (8.70)
 9     13    139     32 ( 20.25)     2  0    0   0   0   1     1 (7.69)    3    3 (9.38)
 8      9    148     19 ( 12.03)     0  0    0   1   0   0     1 (11.11)    4    2 (10.53)
 7      8    156     10 (  6.33)     0  0    0   0   0   1     1 (12.50)    5    1 (10.00)
 6      2    158      2 (  1.27)     0  0    0   0   0   0     0 (0.00)    5    0 (0.00)
-1      5    163      0 (  0.00)    25  0    0   0   0   0     0 (0.00)    5    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    163    163      0 (  0.00)    28  0    0   2   0   3     5 (3.07)    5    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      49       49        1

SS region: 49 (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     ae050109r1      (0)/(0)  11 GCC / GGC
    18  D     ae050109r1      (0)/(0)  15 GGTGG / GTTG
    18  D     bg070109r1      (0)/(0)  14 GGGTGG / GGTG

0 HQ discrepancies in 0 reads.
3 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.  8 reads; 44 bp (untrimmed), 0 (trimmed).  Isolated contig.
     -6   957 bc120109r1     29 (  0)  0.00 0.00 0.00   21 ( 20)  913 (913) 
     -5   948 bh110109r1     26 (  0)  3.12 3.12 0.00   18 (  8)  904 (904) 
     -2   984 ag070109r1     29 (  0)  0.00 0.00 0.00   17 (  4)  940 (940) 
     -2   972 bb090109r1     27 (  0)  2.44 4.88 0.00    6 (  6)  928 (928) 
     -1   971 ba040109r1     30 (  0)  5.13 0.00 0.00    7 (  5)  927 (927) 
     -1   967 ba010109r1     29 (  0)  0.00 0.00 0.00   16 (  4)  923 (923) 
      0   997 bf050109r1     37 (  0)  0.00 2.27 0.00    1 (  4)  953 (953) 
      0   981 bc060109r1     35 (  0)  2.27 2.27 0.00    1 (  6)  937 (937) 

Overall discrep rates (%):             1.72 1.72 0.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 -1      44 100.0      44 100.0   44.00   (quality -1 = terminal quality 0)

Avg. full length: 44.0, trimmed (qual > -1): 0.0
Avg. quality: 0.0 per base

Initial, terminal qual 0 segments:  1-44, (None)

Regions of LLR- adjusted quality < 2.0:
1-44, 

1 regions, avg size 44.0, avg spacing 44.0

First_start: 4, last_end: 44

Slack, # used pairs (max_score), unused
 0    11  ( 0.0)     0 ( 0.0)       12
 1     1  ( 0.0)     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+
   45 - right        0+      bf050109r1   (   0)    No             44+

Bottom strand: 
 left - right       44+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56      4      4    295 (100.00)     0  0    0   0   0   0     0 (0.00)    0   10 (3.39)
51      1      5    291 ( 98.64)     0  0    0   0   0   0     0 (0.00)    0   10 (3.44)
48      1      6    290 ( 98.31)     0  0    0   0   0   0     0 (0.00)    0   10 (3.45)
46      9     15    289 ( 97.97)     0  0    0   0   0   0     0 (0.00)    0   10 (3.46)
44      1     16    280 ( 94.92)     0  0    0   0   0   0     0 (0.00)    0   10 (3.57)
42      1     17    279 ( 94.58)     0  0    0   0   0   0     0 (0.00)    0   10 (3.58)
40     13     30    278 ( 94.24)     0  0    0   0   0   0     0 (0.00)    0   10 (3.60)
39      3     33    265 ( 89.83)     0  0    0   0   0   0     0 (0.00)    0   10 (3.77)
37      1     34    262 ( 88.81)     0  0    0   0   0   0     0 (0.00)    0   10 (3.82)
34      1     35    261 ( 88.47)     0  0    0   0   0   0     0 (0.00)    0   10 (3.83)
33      1     36    260 ( 88.14)     0  0    0   0   0   0     0 (0.00)    0   10 (3.85)
32      7     43    259 ( 87.80)     0  0    0   0   0   0     0 (0.00)    0   10 (3.86)
30      1     44    252 ( 85.42)     0  0    0   0   0   0     0 (0.00)    0   10 (3.97)
29     13     57    251 ( 85.08)     0  0    0   0   0   0     0 (0.00)    0   10 (3.98)
28      2     59    238 ( 80.68)     0  0    0   0   0   0     0 (0.00)    0   10 (4.20)
27      4     63    236 ( 80.00)     0  0    0   0   0   0     0 (0.00)    0   10 (4.24)
26      5     68    232 ( 78.64)     0  0    0   0   0   0     0 (0.00)    0   10 (4.31)
25     21     89    227 ( 76.95)     0  0    0   0   0   0     0 (0.00)    0   10 (4.41)
24      6     95    206 ( 69.83)     0  0    0   0   0   0     0 (0.00)    0   10 (4.85)
23      9    104    200 ( 67.80)     0  0    0   0   0   0     0 (0.00)    0   10 (5.00)
22      7    111    191 ( 64.75)     0  0    0   0   0   0     0 (0.00)    0   10 (5.24)
21      2    113    184 ( 62.37)     1  0    0   0   0   0     0 (0.00)    0   10 (5.43)
20      3    116    182 ( 61.69)     0  0    0   0   0   0     0 (0.00)    0   10 (5.49)
19     11    127    179 ( 60.68)     0  0    0   0   0   0     0 (0.00)    0   10 (5.59)
18      5    132    168 ( 56.95)     0  0    0   0   0   0     0 (0.00)    0   10 (5.95)
17     13    145    163 ( 55.25)     0  0    0   0   0   0     0 (0.00)    0   10 (6.13)
16      9    154    150 ( 50.85)     0  0    0   0   0   0     0 (0.00)    0   10 (6.67)
15     10    164    141 ( 47.80)     0  0    0   0   0   0     0 (0.00)    0   10 (7.09)
14      4    168    131 ( 44.41)     0  0    0   0   0   0     0 (0.00)    0   10 (7.63)
13     19    187    127 ( 43.05)     1  0    0   0   0   0     0 (0.00)    0   10 (7.87)
12     12    199    108 ( 36.61)     1  0    0   0   0   0     0 (0.00)    0   10 (9.26)
11     15    214     96 ( 32.54)     2  0    0   0   0   0     0 (0.00)    0   10 (10.42)
10     12    226     81 ( 27.46)    10  0    0   1   0   0     1 (8.33)    1   10 (12.35)
 9     18    244     69 ( 23.39)     7  0    0   0   0   0     0 (0.00)    1    9 (13.04)
 8     14    258     51 ( 17.29)     4  0    0   0   1   0     1 (7.14)    2    9 (17.65)
 7     13    271     37 ( 12.54)     2  0    0   1   0   0     1 (7.69)    3    8 (21.62)
 6      9    280     24 (  8.14)     9  0    0   2   0   0     2 (22.22)    5    7 (29.17)
 4     10    290     15 (  5.08)     1  0    0   0   0   0     0 (0.00)    5    5 (33.33)
 0      5    295      5 (  1.69)     0  0    1   0   4   0     5 (100.00)   10    5 (100.00)
-1      0    295      0 (  0.00)    24  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 (%)
-1    295    295      0 (  0.00)    62  0    1   4   5   0    10 (3.39)   10    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      44       44        1

SS region: 44 (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):
    27  I     bh110109r1      (0)/(0)  27 AG / ANG
    10  S     bb090109r1      (0)/(0)  9 GCC / GGC
    14  I     bb090109r1      (0)/(0)  14 TG / TTG
    27  I     bb090109r1      (0)/(0)  27 AG / ANG
    14  S     ba040109r1      (0)/(0)  10 CCGGTG / CGGGGG
    27  I     bf050109r1      (0)/(0)  27 AG / ANG
     5  S     bc060109r1      (0)/(0)  4 CCC / CTC
    27  I     bc060109r1      (0)/(0)  27 AG / ANG

0 HQ discrepancies in 0 reads.
8 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 15.  133 reads; 7017 bp (untrimmed), 6987 (trimmed).
    -49   867 a0001g02t7_b03  815 (  0)  0.58 0.12 0.12   50 (277)    6 (  6) 
    182  1149 ag020109r1    727 (  0)  1.13 0.50 0.00   46 ( 46)  129 (160) 
C   231  1217 ab030109f1     19 (  0)  0.00 0.00 0.00  887 (910)   81 ( 10) 
    238  1221 bg100109f1     99 (  0)  21.68 0.49 0.32   36 ( 36)  330 (904) 
C   283  1276 ag020109f1    267 (  0)  15.12 1.03 0.59  284 (467)   29 (286) 
   1023  2020 ab030109r1     39 (  0)  0.00 0.00 0.00   86 ( 98)  872 (811) 
   1094  2079 bb080109f1    778 (  0)  1.36 0.80 0.00  104 ( 26)    2 ( 47) 
   1133  2124 ae010109f1     17 (  0)  26.09 0.00 0.00  136 ( 27)  373 (909) 
   1282  2248 aa100109f1    659 (  0)  4.07 1.98 0.23   27 (134)   81 (179) 
   1574  2589 ab040109f1    771 (  0)  1.59 1.36 0.11   19 ( 19)  115 (145) 
   1642  2620 ab060109f1    813 (  0)  2.96 0.74 0.11   26 ( 26)    7 (122) 
   1654  2649 ag090109f1    695 (  0)  1.43 0.65 0.13   22 ( 22)  205 (214) 
C  1763  2762 bg100109r1    558 (  0)  3.38 2.39 0.00  235 (309)   54 ( 89) 
   1780  2808 ah120109f1    393 (  0)  9.44 1.18 0.17   30 ( 30)  406 (453) 
   1811  2773 ae090109r1    858 (  0)  0.77 0.55 0.00   48 ( 48)    1 (  6) 
   1816  2792 bd020109f1    811 (  0)  1.17 1.92 0.11   24 ( 24)   16 (120) 
   1882  2940 bc080109f1    666 (  0)  1.17 1.95 0.00   25 ( 25)  265 (317) 
   1915  2905 bd090109f1    488 (  0)  0.00 0.00 0.39   26 ( 26)  456 (456) 
   2037  3015 ae070109f1    849 (  0)  1.26 0.95 0.00   24 ( 24)    6 ( 17) 
   2044  3024 bg080109r1    812 (  0)  0.55 1.54 0.00   46 ( 46)   25 ( 25) 
   2063  3056 bh100109r1    404 (  0)  9.60 0.80 0.32   55 ( 55)  314 (573) 
   2254  3301 bc090109f1    155 (  0)  3.14 0.00 1.05   25 ( 25)  832 (836) 
   2359  3333 ba060109r1    798 (  0)  1.08 0.87 0.00   51 ( 51)    0 (  0) 
   2387  3350 ad070109r1    831 (  0)  0.43 0.33 0.00   43 ( 43)    1 (  1) 
C   -17   951 ae010109r1      4 (  0)  25.00 0.00 0.00  427 (887)  530 ( 60) 
   2587  3521 ag110109r1    800 (  0)  0.45 0.00 0.00   45 ( 45)    0 (  4) 
   2654  3630 bb070109f1    855 (  0)  0.21 0.53 0.00   25 ( 25)    3 (  3) 
C  2678  3669 ab040109r1    789 (  0)  1.06 1.38 0.00    3 (  3)   48 ( 46) 
C  2687  3658 ba060109f1    836 (  0)  0.42 0.32 0.21    0 (  0)   30 ( 30) 
   2846  3828 bb060109r1    815 (  0)  1.29 0.86 0.00   46 ( 46)    5 ( 37) 
C  2878  3849 ad070109f1    871 (  0)  0.85 0.00 0.00    2 (  0)   24 ( 24) 
   2903  3878 bg040109f1    857 (  0)  0.54 0.22 0.00   28 ( 28)   26 ( 26) 
   2906  3867 aa050109r1    867 (  0)  0.11 0.00 0.00   51 ( 51)    0 (  0) 
   2935  3891 ba020109f1    884 (  0)  0.00 0.11 0.11   23 ( 23)    1 (  0) 
   2944  3911 ae100109f1    746 (  0)  3.90 0.76 0.11   26 ( 26)   20 ( 57) 
   2983  3952 ac050109r1    819 (  0)  0.89 0.66 0.11   46 ( 46)   21 ( 46) 
C  3001  3965 ae090109f1    882 (  0)  0.43 0.21 0.00    2 ( 10)   25 ( 25) 
C  3010  3977 bc020109r1    885 (  0)  0.00 0.00 0.00    1 (  1)   47 ( 47) 
C  3041  4016 bd090109r1    841 (  0)  0.55 0.66 0.00   21 ( 55)   46 ( 46) 
   3092  4066 bg050109f1    870 (  0)  0.74 0.53 0.21   23 ( 23)    8 ( 40) 
   3096  4040 ab110109r1    786 (  0)  1.36 1.14 0.00   47 ( 47)   17 ( 82) 
   3160  4135 af060109r1    884 (  0)  0.65 0.22 0.00   46 ( 43)    5 ( 14) 
C  3175  4120 aa100109r1    830 (  0)  0.67 0.89 0.00    0 (  0)   48 ( 48) 
   3172  4140 ba090109r1    822 (  0)  0.78 1.22 0.00   47 ( 47)   24 ( 84) 
   3178  4202 bc040109f1    802 (  0)  0.12 0.36 0.00   28 ( 19)  166 (166) 
   3178  4173 ac040109f1    883 (  0)  1.15 0.63 0.10   28 ( 19)   10 ( 10) 
   3229  4186 af090109r1    873 (  0)  0.44 0.33 0.00   48 ( 48)    0 (  0) 
C  3271  4243 ae070109r1    900 (  0)  0.11 0.22 0.00    3 (  8)   46 ( 46) 
   3560  4554 ad080109f1    632 (  0)  4.50 1.62 0.12   26 ( 26)  169 (355) 
C  3575  4549 bc110109r1    790 (  0)  1.16 1.04 0.00   63 ( 89)   48 ( 48) 
   3580  4565 bh080109f1    789 (  0)  1.87 1.21 0.33   26 ( 26)   52 ( 91) 
C  3602  4559 ag090109r1    872 (  0)  0.99 0.11 0.00    0 (  0)   46 ( 46) 
   3627  4651 ab090109f1    619 (  0)  2.69 1.88 0.13   25 ( 25)  256 (288) 
C  3656  4623 ab060109r1    899 (  0)  0.33 0.11 0.00    0 (  0)   45 ( 45) 
   3658  4604 ac110109r1    881 (  0)  0.22 0.11 0.00   47 ( 47)    0 (  0) 
C  3710  4667 ab090109r1    875 (  0)  0.33 0.44 0.00    2 (  2)   46 ( 46) 
C  3809  4784 bg080109f1    892 (  0)  0.53 0.63 0.11    3 (  3)   26 ( 25) 
C  3812  4772 bh100109f1    848 (  0)  1.18 1.07 0.00    4 (  4)   25 ( 25) 
C  3824  4791 aa050109f1    827 (  0)  1.28 1.60 0.11    3 (  3)   27 ( 27) 
C  3864  4841 bc090109r1    918 (  0)  0.21 0.11 0.00    0 (  0)   39 ( 39) 
C  3882  4854 bd020109r1    903 (  0)  0.22 0.11 0.00    0 (  5)   48 ( 48) 
C  3908  4853 ah120109r1    835 (  0)  0.89 0.67 0.11    0 (  6)   47 ( 47) 
   3933  4901 ba070109r1    846 (  0)  0.99 0.44 0.11   51 ( 51)    6 (  6) 
   4070  4948 ad100109f1    352 (  0)  3.02 0.22 2.38   26 ( 26)  390 (466) 
   4152  5120 bf100109f1    861 (  0)  1.27 0.21 0.11   24 ( 24)    1 (  8) 
   4170  5189 aa040109f1    650 (  0)  1.17 2.08 0.00   27 ( 27)  224 (224) 
   4172  5126 be010109f1    829 (  0)  1.31 0.54 0.00   26 ( 26)   10 ( 10) 
   4195  5148 bh120109f1    868 (  0)  0.22 0.11 0.22   30 ( 30)    1 (  1) 
C  4240  5179 ag110109f1    786 (  0)  1.88 0.66 0.11   14 ( 48)   23 ( 23) 
   4293  5262 bh060109f1    850 (  0)  0.53 0.75 0.00   25 ( 25)    9 (  9) 
   4296  5273 ah040109r1    591 (  0)  2.64 0.44 0.00   53 ( 53)  244 (244) 
   4330  5309 bb030109f1    863 (  0)  0.52 0.84 0.10   26 ( 26)    0 ( 23) 
C  4347  5320 bb070109r1    864 (  0)  0.54 0.11 0.11    2 (  2)   44 ( 44) 
   4367  5308 af120109f1    814 (  0)  0.11 1.12 0.00   29 ( 40)   20 ( 20) 
C  4519  5494 af060109f1    861 (  0)  0.32 1.05 0.11    2 (  2)   23 ( 22) 
C  4527  5497 ac050109f1    865 (  0)  1.06 0.32 0.00    0 (  0)   26 ( 25) 
C  4551  5512 bg040109r1    857 (  0)  0.66 0.11 0.00    5 (  4)   43 ( 43) 
C  4593  5568 bb080109r1    836 (  0)  1.18 0.65 0.00    0 (  9)   47 ( 47) 
C  4607  5573 ad080109r1    866 (  0)  0.54 0.11 0.00    0 (  0)   47 ( 47) 
C  4632  5608 bb060109f1    856 (  0)  1.58 0.32 0.00    4 ( 17)   26 ( 26) 
C  4663  5640 bc080109r1    858 (  0)  0.54 0.65 0.00    4 (  4)   44 ( 44) 
   4701  5661 bd010109r1    864 (  0)  0.00 0.55 0.00   47 ( 47)    0 (  0) 
   4731  5704 bg120109f1    795 (  0)  0.34 1.03 0.00   27 ( 27)   74 ( 74) 
   4800  5785 ab050109f1    733 (  0)  3.68 2.10 0.00   27 ( 27)    8 ( 88) 
   4859  5829 bh070109r1    816 (  0)  1.51 0.97 0.00   45 ( 45)    0 ( 23) 
   5154  6131 ab070109f1    900 (  0)  0.53 0.11 0.00   25 ( 25)    5 (  5) 
C  5163  6122 ba020109r1    808 (  0)  1.11 0.89 0.11    7 ( 41)   50 ( 50) 
C  5178  6161 ba070109f1    689 (  0)  0.85 2.54 0.24  133 (230)   24 ( 24) 
C  5192  6153 ba090109f1    799 (  0)  1.28 1.82 0.11    2 ( 69)   26 ( 26) 
C  5261  6239 bh080109r1    721 (  0)  2.24 2.24 0.11   38 (146)   48 ( 48) 
C  5305  6294 bc040109r1    728 (  0)  3.30 0.47 0.12   98 (157)   44 ( 44) 
C  5315  6297 ac040109r1    831 (  0)  1.82 0.75 0.11    0 ( 86)   47 ( 47) 
C  5335  6288 bh120109r1    735 (  0)  2.47 0.56 1.01   19 (115)   45 ( 43) 
   5341  6316 ae040109r1    885 (  0)  0.32 0.32 0.00   48 ( 48)    4 (  4) 
C  5359  6309 be010109r1    855 (  0)  0.45 0.11 0.00   15 ( 13)   46 ( 46) 
C  5380  6331 af090109f1    814 (  0)  1.65 0.77 0.11   20 ( 99)   21 ( 21) 
   5393  6346 bd120109f1    901 (  0)  0.22 0.00 0.00   26 ( 26)    0 (  0) 
   5435  6426 bd040109r1    903 (  0)  0.32 0.11 0.00   47 ( 46)    0 (  0) 
C  5452  6399 ab110109f1    791 (  0)  1.47 0.90 0.00   33 ( 60)   28 ( 28) 
   5553  6534 ac090109f1    855 (  0)  1.17 0.64 0.00   27 ( 17)   11 ( 11) 
   5555  6529 bg090109f1    873 (  0)  0.84 0.42 0.11   25 ( 15)    0 ( 17) 
C  5570  6529 aa040109r1    842 (  0)  0.22 0.99 0.00    0 (  6)   47 ( 47) 
C  5571  6528 bd010109f1    885 (  0)  0.43 0.00 0.11    0 (  0)   27 ( 27) 
   5613  6584 ad060109f1    851 (  0)  1.27 0.74 0.00   24 ( 24)    0 ( 58) 
C  5700  6722 ab050109r1    618 (  0)  2.23 0.70 0.00  261 (265)   46 ( 46) 
C  5816  6787 ae040109f1    878 (  0)  0.32 0.63 0.00    0 (  0)   27 ( 27) 
C  5834  6791 ad100109r1    859 (  0)  0.00 0.44 0.00    0 (  0)   49 ( 49) 
C  5863  6791 af120109r1    834 (  0)  0.45 0.11 0.00    0 ( 11)   45 ( 45) 
C  5914  6880 bf100109r1    874 (  0)  0.33 0.00 0.22    1 (  1)   45 ( 45) 
C  6014  6991 bb030109r1    882 (  0)  0.11 0.43 0.00    5 (  3)   46 ( 46) 
C  6109  7029 a0001g02sp6_e03  668 (  0)  3.00 3.44 0.11    0 ( 60)   21 ( 21) 
   6129  7122 be060109f1    838 (  0)  0.12 0.00 0.00   26 ( 26)  105 (105) 
   6147  7127 bb090109f1    812 (  0)  0.24 0.12 0.00   23 ( 23)  113 ( 76) 
   6165  7151 bg070109f1    801 (  0)  0.24 0.00 0.00   27 ( 27)  134 (134) 
C  6175  7160 bd040109f1    789 (  0)  0.48 0.12 0.36    2 (  7)  143 (143) 
   6189  7162 bg020109f1    787 (  0)  0.00 0.00 0.00   23 ( 22)  145 (145) 
C  6215  7183 ab070109r1    549 (  0)  0.35 0.17 0.00    3 (  3)  390 (390) 
   6223  7189 ac120109f1    689 (  0)  1.43 0.91 0.00   26 ( 26)  172 (138) 
   6355  7330 bh090109f1    603 (  0)  0.94 0.00 0.00   26 ( 26)  313 (313) 
   6419  7391 bf010109f1    537 (  0)  0.53 0.00 0.35   31 ( 31)  374 (374) 
C  6430  7417 bg050109r1    452 (  0)  1.14 1.90 0.19   63 ( 63)  400 (400) 
   6441  7438 af020109f1     21 (  0)  40.23 0.87 0.29   28 ( 28)  627 (918) 
C  6487  7457 ac090109r1    472 (  0)  1.90 0.38 0.19    6 ( 28)  440 (440) 
   6529  7561 ae080109f1    439 (  0)  0.87 0.00 0.22   27 ( 29)  544 (544) 
   6605  7697 ab010109f1    101 ( 74)  23.19 0.00 0.58   22 ( 22)  726 (734) 
C  6617  7586 bh070109f1    346 (251)  1.50 1.75 0.00    1 ( 37)  569 (569) 
C  6644  7609 bh060109r1    310 (282)  2.15 2.15 0.00    2 ( 22)  592 (592) 
C  6701  7651 bd120109r1    231 (215)  4.73 2.21 0.63    0 (  0)  634 (634) 
C  6819  7789 bg090109r1     92 ( 88)  7.43 2.86 2.29   24 ( 79)  772 (772) 
   6841  8028 ae030109f1    129 (118)  3.85 0.00 0.64   21 ( 21) 1011 (1011) 
   6863  7916 ah070109f1     70 ( 60)  13.33 0.74 0.00   20 ( 24)  899 (940) 
   6883  7868 aa060109f1     79 ( 72)  4.72 0.94 0.00   29 ( 29)  851 (851) 
C  6952  7925 ad060109r1     32 (  0)  4.76 7.94 0.00    0 ( 21)  911 (902) 

Overall discrep rates (%):             1.70 0.70 0.09

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90    4349  62.0    4349  62.0    0.00
 89      14   0.2    4363  62.2    0.00
 88      19   0.3    4382  62.4    0.00
 87      27   0.4    4409  62.8    0.00
 86      13   0.2    4422  63.0    0.00
 85      26   0.4    4448  63.4    0.00
 84      24   0.3    4472  63.7    0.00
 83      23   0.3    4495  64.1    0.00
 82      23   0.3    4518  64.4    0.00
 81     125   1.8    4643  66.2    0.00
 80       5   0.1    4648  66.2    0.00
 79      16   0.2    4664  66.5    0.00
 78       8   0.1    4672  66.6    0.00
 77      19   0.3    4691  66.9    0.00
 76      23   0.3    4714  67.2    0.00
 75      21   0.3    4735  67.5    0.00
 74       9   0.1    4744  67.6    0.00
 73       3   0.0    4747  67.6    0.00
 72       3   0.0    4750  67.7    0.00
 71       2   0.0    4752  67.7    0.00
 66    1024  14.6    5776  82.3    0.00
 65       1   0.0    5777  82.3    0.00
 61     104   1.5    5881  83.8    0.00
 60      62   0.9    5943  84.7    0.00
 59       2   0.0    5945  84.7    0.00
 58       9   0.1    5954  84.9    0.00
 57      10   0.1    5964  85.0    0.00
 56     292   4.2    6256  89.2    0.00
 55      27   0.4    6283  89.5    0.00
 54      36   0.5    6319  90.1    0.00
 53      14   0.2    6333  90.3    0.00
 52      32   0.5    6365  90.7    0.00
 51     144   2.1    6509  92.8    0.00
 50      16   0.2    6525  93.0    0.00
 49       2   0.0    6527  93.0    0.00
 48       3   0.0    6530  93.1    0.00
 47       3   0.0    6533  93.1    0.00
 46       8   0.1    6541  93.2    0.00
 45      25   0.4    6566  93.6    0.00
 44      13   0.2    6579  93.8    0.00
 43      11   0.2    6590  93.9    0.01
 42      13   0.2    6603  94.1    0.01
 40      24   0.3    6627  94.4    0.01
 39       5   0.1    6632  94.5    0.01
 38       5   0.1    6637  94.6    0.01
 37      12   0.2    6649  94.8    0.01
 35       9   0.1    6658  94.9    0.02
 34       4   0.1    6662  94.9    0.02
 33      12   0.2    6674  95.1    0.02
 32       7   0.1    6681  95.2    0.03
 31       5   0.1    6686  95.3    0.03
 30       9   0.1    6695  95.4    0.04
 29       9   0.1    6704  95.5    0.05
 28       8   0.1    6712  95.7    0.06
 27       6   0.1    6718  95.7    0.08
 26       5   0.1    6723  95.8    0.09
 25       5   0.1    6728  95.9    0.10
 24       5   0.1    6733  96.0    0.12
 23       8   0.1    6741  96.1    0.16
 22       6   0.1    6747  96.2    0.20
 21       4   0.1    6751  96.2    0.23
 20       7   0.1    6758  96.3    0.30
 19       7   0.1    6765  96.4    0.39
 18       4   0.1    6769  96.5    0.46
 17       5   0.1    6774  96.5    0.56
 16       9   0.1    6783  96.7    0.78
 15       4   0.1    6787  96.7    0.91
 14       1   0.0    6788  96.7    0.95
 13       9   0.1    6797  96.9    1.40
 12       2   0.0    6799  96.9    1.52
 11       1   0.0    6800  96.9    1.60
 10       5   0.1    6805  97.0    2.10
  9       5   0.1    6810  97.1    2.73
  8       4   0.1    6814  97.1    3.37
  7       1   0.0    6815  97.1    3.57
  0     172   2.5    6987  99.6  175.57
 -1      30   0.4    7017 100.0  205.57   (quality -1 = terminal quality 0)

Avg. full length: 7017.0, trimmed (qual > -1): 6987.0
Avg. quality: 77.3 per base

Initial, terminal qual 0 segments:  1-30, (None)

Regions of LLR- adjusted quality < 2.0:
1-30, 773-774, 780-781, 807, 809, 866-871, 878-880, 882, 
889-890, 904-908, 922-925, 927-929, 931-933, 936-939, 941-943, 945-946, 
949, 954-955, 990-1116, 1137-1144, 1149-1197, 

22 regions, avg size 11.8, avg spacing 319.0

First_start: 228, last_end: 7051

Slack, # used pairs (max_score), unused
 0   646  (20.1)     0 ( 0.0)     1874
 1   709  (20.4)     0 ( 0.0)      226
 2   308  (19.9)     0 ( 0.0)        5
 3   171  (19.6)     0 ( 0.0)        0
 4   109  (19.5)     0 ( 0.0)        0
 5    56  (18.9)     0 ( 0.0)        0
 6    46  (16.7)     0 ( 0.0)        0
 7    17  (18.3)     0 ( 0.0)        0
 8    13  (15.7)     0 ( 0.0)        0
 9    10  (11.2)     0 ( 0.0)        0
10     5  ( 9.7)     0 ( 0.0)        0
11     4  (12.7)     0 ( 0.0)        0
12     3  ( 8.4)     0 ( 0.0)        0
13     1  (13.4)     0 ( 0.0)        0
14     2  (12.3)     0 ( 0.0)        0
99     5  ( 4.4)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 
WARNING: 34 bases of confirmed read sequence omitted from right end of contig

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 1021 -  1108       88       bg100109f1   ( 238)    Yes           871
 1149 -  1197       49       ae010109f1   (1133)    Yes            65
 7018 - right        0+      aa060109f1   (6883)    No            134+

Bottom strand: 
 left -   566      566+      ae010109r1   ( 951)    Yes           951+
 1248 -  1997      750       bg100109r1   (2762)    No           1515 
 7018 - 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  38486  38486 105718 (100.00)   203  0    0   0   0   0     0 (0.00)    0  2600 (2.46)
51  11866  50352  67232 ( 63.60)    72  0    0   1   0   0     1 (0.01)    1  2600 (3.87)
50   1084  51436  55366 ( 52.37)     0  0    0   0   0   0     0 (0.00)    1  2599 (4.69)
48    747  52183  54282 ( 51.35)    40  0    0   0   0   0     0 (0.00)    1  2599 (4.79)
47    237  52420  53535 ( 50.64)     5  0    0   0   0   0     0 (0.00)    1  2599 (4.85)
46   1189  53609  53298 ( 50.42)    45  0    0   0   0   0     0 (0.00)    1  2599 (4.88)
45   2290  55899  52109 ( 49.29)    11  0    0   0   0   0     0 (0.00)    1  2599 (4.99)
44   1356  57255  49819 ( 47.12)    17  0    0   0   0   0     0 (0.00)    1  2599 (5.22)
43    952  58207  48463 ( 45.84)     3  0    0   0   0   0     0 (0.00)    1  2599 (5.36)
42   2531  60738  47511 ( 44.94)    22  0    0   0   0   0     0 (0.00)    1  2599 (5.47)
41    205  60943  44980 ( 42.55)     0  0    0   0   0   0     0 (0.00)    1  2599 (5.78)
40   4896  65839  44775 ( 42.35)   101  0    0   0   0   1     1 (0.02)    2  2599 (5.80)
39    503  66342  39879 ( 37.72)     8  0    0   0   0   0     0 (0.00)    2  2598 (6.51)
38    177  66519  39376 ( 37.25)     2  0    0   0   0   0     0 (0.00)    2  2598 (6.60)
37   1399  67918  39199 ( 37.08)    14  0    0   0   0   0     0 (0.00)    2  2598 (6.63)
36    171  68089  37800 ( 35.76)     2  0    0   0   0   0     0 (0.00)    2  2598 (6.87)
35   1431  69520  37629 ( 35.59)    31  0    0   0   0   0     0 (0.00)    2  2598 (6.90)
34    800  70320  36198 ( 34.24)    16  0    0   0   0   0     0 (0.00)    2  2598 (7.18)
33    914  71234  35398 ( 33.48)    19  0    0   1   1   0     2 (0.22)    4  2598 (7.34)
32    948  72182  34484 ( 32.62)    47  0    0   0   2   0     2 (0.21)    6  2596 (7.53)
31    368  72550  33536 ( 31.72)    12  0    0   0   0   0     0 (0.00)    6  2594 (7.73)
30    499  73049  33168 ( 31.37)    10  0    0   0   0   0     0 (0.00)    6  2594 (7.82)
29   1762  74811  32669 ( 30.90)    93  0    0   0   3   0     3 (0.17)    9  2594 (7.94)
28    511  75322  30907 ( 29.24)    18  0    0   0   0   0     0 (0.00)    9  2591 (8.38)
27    891  76213  30396 ( 28.75)    66  0    0   1   0   0     1 (0.11)   10  2591 (8.52)
26    369  76582  29505 ( 27.91)    36  0    0   0   1   0     1 (0.27)   11  2590 (8.78)
25   1102  77684  29136 ( 27.56)    85  0    0   1   1   0     2 (0.18)   13  2589 (8.89)
24    868  78552  28034 ( 26.52)    43  0    0   1   4   0     5 (0.58)   18  2587 (9.23)
23    764  79316  27166 ( 25.70)    56  0    0   0   4   0     4 (0.52)   22  2582 (9.50)
22    626  79942  26402 ( 24.97)    50  0    0   1   6   0     7 (1.12)   29  2578 (9.76)
21    911  80853  25776 ( 24.38)    57  0    0   1   5   2     8 (0.88)   37  2571 (9.97)
20    872  81725  24865 ( 23.52)    71  0    0   1   7   1     9 (1.03)   46  2563 (10.31)
19   1274  82999  23993 ( 22.70)    95  0    0   6  12   0    18 (1.41)   64  2554 (10.64)
18    947  83946  22719 ( 21.49)    64  0    0   2   7   2    11 (1.16)   75  2536 (11.16)
17    996  84942  21772 ( 20.59)    59  0    0  10  11   1    22 (2.21)   97  2525 (11.60)
16   1064  86006  20776 ( 19.65)    71  0    0   9  11   0    20 (1.88)  117  2503 (12.05)
15   1292  87298  19712 ( 18.65)    95  0    0  10  17   3    30 (2.32)  147  2483 (12.60)
14   1080  88378  18420 ( 17.42)    42  0    0  22  19   1    42 (3.89)  189  2453 (13.32)
13   1535  89913  17340 ( 16.40)    87  0    0  41  18   1    60 (3.91)  249  2411 (13.90)
12   1485  91398  15805 ( 14.95)    51  0    0  50  30   3    83 (5.59)  332  2351 (14.88)
11   2139  93537  14320 ( 13.55)    76  0    0 102  50   5   157 (7.34)  489  2268 (15.84)
10   2481  96018  12181 ( 11.52)   114  0    0 135  82  12   229 (9.23)  718  2111 (17.33)
 9   4169 100187   9700 (  9.18)   184  0    0 350 124  27   501 (12.02)  1219  1882 (19.40)
 8   2168 102355   5531 (  5.23)   101  0    0 268 108  20   396 (18.27)  1615  1381 (24.97)
 7   1783 104138   3363 (  3.18)    71  0    0 268 104   7   379 (21.26)  1994  985 (29.29)
 6    856 104994   1580 (  1.49)    72  0    0 193  65   6   264 (30.84)  2258  606 (38.35)
 4    534 105528    724 (  0.68)   171  0    0 140  12   2   154 (28.84)  2412  342 (47.24)
 0    190 105718    190 (  0.18)   132  0   172   0  15   1   188 (98.95)  2600  188 (98.95)
-1     18 105736      0 (  0.00)  11702  0    3   0   1   0     4 (22.22)  2604    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  77845  77845 100956 (100.00)    24  0    0   0   0   0     0 (0.00)    0  1509 (1.49)
89    107  77952  23111 ( 22.89)     0  0    0   0   0   0     0 (0.00)    0  1509 (6.53)
88    139  78091  23004 ( 22.79)     1  0    0   0   0   0     0 (0.00)    0  1509 (6.56)
87    211  78302  22865 ( 22.65)     0  0    0   0   0   0     0 (0.00)    0  1509 (6.60)
86     87  78389  22654 ( 22.44)     0  0    0   0   0   0     0 (0.00)    0  1509 (6.66)
85    189  78578  22567 ( 22.35)     2  0    0   0   0   0     0 (0.00)    0  1509 (6.69)
84    192  78770  22378 ( 22.17)     2  0    0   0   0   0     0 (0.00)    0  1509 (6.74)
83    183  78953  22186 ( 21.98)     2  0    0   0   0   0     0 (0.00)    0  1509 (6.80)
82    146  79099  22003 ( 21.79)     0  0    0   0   0   0     0 (0.00)    0  1509 (6.86)
81   1109  80208  21857 ( 21.65)     0  0    0   0   0   0     0 (0.00)    0  1509 (6.90)
80     18  80226  20748 ( 20.55)     1  0    0   0   0   0     0 (0.00)    0  1509 (7.27)
79     34  80260  20730 ( 20.53)     0  0    0   0   0   0     0 (0.00)    0  1509 (7.28)
78     17  80277  20696 ( 20.50)     1  0    0   0   0   0     0 (0.00)    0  1509 (7.29)
77     47  80324  20679 ( 20.48)     0  0    0   0   0   0     0 (0.00)    0  1509 (7.30)
76    145  80469  20632 ( 20.44)     0  0    0   0   0   0     0 (0.00)    0  1509 (7.31)
75     47  80516  20487 ( 20.29)     0  0    0   0   0   0     0 (0.00)    0  1509 (7.37)
74     14  80530  20440 ( 20.25)     0  0    0   0   0   0     0 (0.00)    0  1509 (7.38)
73     42  80572  20426 ( 20.23)     1  0    0   0   0   0     0 (0.00)    0  1509 (7.39)
72      7  80579  20384 ( 20.19)     0  0    0   0   0   0     0 (0.00)    0  1509 (7.40)
71     46  80625  20377 ( 20.18)     3  0    0   0   0   0     0 (0.00)    0  1509 (7.41)
70     26  80651  20331 ( 20.14)     0  0    0   0   0   0     0 (0.00)    0  1509 (7.42)
69     52  80703  20305 ( 20.11)     1  0    0   0   0   0     0 (0.00)    0  1509 (7.43)
68      2  80705  20253 ( 20.06)     0  0    0   0   0   0     0 (0.00)    0  1509 (7.45)
67     25  80730  20251 ( 20.06)     2  0    0   0   0   0     0 (0.00)    0  1509 (7.45)
66   5802  86532  20226 ( 20.03)    38  0    0   0   0   0     0 (0.00)    0  1509 (7.46)
65    220  86752  14424 ( 14.29)     2  0    0   0   0   0     0 (0.00)    0  1509 (10.46)
64     29  86781  14204 ( 14.07)     0  0    0   0   0   0     0 (0.00)    0  1509 (10.62)
63      7  86788  14175 ( 14.04)     0  0    0   0   0   0     0 (0.00)    0  1509 (10.65)
62     42  86830  14168 ( 14.03)     0  0    0   0   0   0     0 (0.00)    0  1509 (10.65)
61    399  87229  14126 ( 13.99)    11  0    0   0   0   0     0 (0.00)    0  1509 (10.68)
60    185  87414  13727 ( 13.60)     0  0    0   0   0   0     0 (0.00)    0  1509 (10.99)
59     50  87464  13542 ( 13.41)     2  0    0   0   0   0     0 (0.00)    0  1509 (11.14)
58     61  87525  13492 ( 13.36)     1  0    0   0   0   0     0 (0.00)    0  1509 (11.18)
57    113  87638  13431 ( 13.30)     1  0    0   0   0   0     0 (0.00)    0  1509 (11.24)
56    413  88051  13318 ( 13.19)   185  0    0   0   0   0     0 (0.00)    0  1509 (11.33)
55     81  88132  12905 ( 12.78)     4  0    0   0   0   0     0 (0.00)    0  1509 (11.69)
54    184  88316  12824 ( 12.70)     7  0    0   0   0   0     0 (0.00)    0  1509 (11.77)
53     64  88380  12640 ( 12.52)     0  0    0   0   0   0     0 (0.00)    0  1509 (11.94)
52    148  88528  12576 ( 12.46)     4  0    0   0   0   0     0 (0.00)    0  1509 (12.00)
51    198  88726  12428 ( 12.31)    56  0    0   1   0   0     1 (0.51)    1  1509 (12.14)
50    175  88901  12230 ( 12.11)    31  0    0   0   0   0     0 (0.00)    1  1508 (12.33)
49     98  88999  12055 ( 11.94)     8  0    0   0   0   0     0 (0.00)    1  1508 (12.51)
48     89  89088  11957 ( 11.84)     0  0    0   0   0   0     0 (0.00)    1  1508 (12.61)
47     60  89148  11868 ( 11.76)     4  0    0   0   0   0     0 (0.00)    1  1508 (12.71)
46    139  89287  11808 ( 11.70)     2  0    0   0   0   0     0 (0.00)    1  1508 (12.77)
45    168  89455  11669 ( 11.56)     5  0    0   0   0   0     0 (0.00)    1  1508 (12.92)
44    168  89623  11501 ( 11.39)     7  0    0   0   0   0     0 (0.00)    1  1508 (13.11)
43    114  89737  11333 ( 11.23)     0  0    0   0   0   0     0 (0.00)    1  1508 (13.31)
42    176  89913  11219 ( 11.11)     6  0    0   0   0   0     0 (0.00)    1  1508 (13.44)
41    182  90095  11043 ( 10.94)     0  0    0   0   0   0     0 (0.00)    1  1508 (13.66)
40   2361  92456  10861 ( 10.76)    10  0    0   0   1   1     2 (0.08)    3  1508 (13.88)
39     47  92503   8500 (  8.42)     3  0    0   0   0   0     0 (0.00)    3  1506 (17.72)
38     36  92539   8453 (  8.37)     3  0    0   0   0   0     0 (0.00)    3  1506 (17.82)
37     66  92605   8417 (  8.34)     8  0    0   0   0   0     0 (0.00)    3  1506 (17.89)
36     40  92645   8351 (  8.27)     1  0    0   0   2   0     2 (5.00)    5  1506 (18.03)
35     92  92737   8311 (  8.23)     2  0    0   0   0   0     0 (0.00)    5  1504 (18.10)
34    110  92847   8219 (  8.14)     5  0    0   0   3   0     3 (2.73)    8  1504 (18.30)
33     76  92923   8109 (  8.03)     5  0    0   0   2   0     2 (2.63)   10  1501 (18.51)
32     73  92996   8033 (  7.96)     6  0    0   0   2   0     2 (2.74)   12  1499 (18.66)
31     42  93038   7960 (  7.88)     5  0    0   0   0   0     0 (0.00)   12  1497 (18.81)
30     48  93086   7918 (  7.84)     7  0    0   0   0   0     0 (0.00)   12  1497 (18.91)
29    112  93198   7870 (  7.80)     5  0    0   0   4   0     4 (3.57)   16  1497 (19.02)
28     48  93246   7758 (  7.68)     4  0    0   0   1   0     1 (2.08)   17  1493 (19.24)
27     71  93317   7710 (  7.64)     3  0    0   0   0   0     0 (0.00)   17  1492 (19.35)
26     73  93390   7639 (  7.57)     1  0    0   0   2   0     2 (2.74)   19  1492 (19.53)
25    340  93730   7566 (  7.49)     8  0    0   1   3   0     4 (1.18)   23  1490 (19.69)
24    112  93842   7226 (  7.16)    10  0    0   0   4   0     4 (3.57)   27  1486 (20.56)
23    107  93949   7114 (  7.05)     5  0    0   0   6   0     6 (5.61)   33  1482 (20.83)
22     65  94014   7007 (  6.94)     7  0    0   1   8   0     9 (13.85)   42  1476 (21.06)
21     94  94108   6942 (  6.88)     5  0    0   0   4   3     7 (7.45)   49  1467 (21.13)
20    105  94213   6848 (  6.78)     6  0    0   0   7   1     8 (7.62)   57  1460 (21.32)
19    195  94408   6743 (  6.68)     8  0    0   1   9   0    10 (5.13)   67  1452 (21.53)
18    111  94519   6548 (  6.49)     5  0    0   1   4   2     7 (6.31)   74  1442 (22.02)
17    181  94700   6437 (  6.38)     9  0    0   5  11   1    17 (9.39)   91  1435 (22.29)
16    204  94904   6256 (  6.20)    12  0    0   3   8   0    11 (5.39)  102  1418 (22.67)
15    240  95144   6052 (  5.99)     5  0    0   7  15   3    25 (10.42)  127  1407 (23.25)
14    233  95377   5812 (  5.76)     7  0    0  13  16   1    30 (12.88)  157  1382 (23.78)
13    411  95788   5579 (  5.53)    12  0    0  16  13   0    29 (7.06)  186  1352 (24.23)
12    355  96143   5168 (  5.12)     5  0    0  27  24   2    53 (14.93)  239  1323 (25.60)
11    520  96663   4813 (  4.77)    18  0    0  51  27   4    82 (15.77)  321  1270 (26.39)
10    761  97424   4293 (  4.25)    20  0    0  78  49  11   138 (18.13)  459  1188 (27.67)
 9   1308  98732   3532 (  3.50)    15  0    0 157  80  17   254 (19.42)  713  1050 (29.73)
 8    759  99491   2224 (  2.20)     6  0    0 172  65  11   248 (32.67)  961  796 (35.79)
 7    817 100308   1465 (  1.45)     6  0    0 191  86   6   283 (34.64)  1244  548 (37.41)
 6    382 100690    648 (  0.64)     1  0    0  99  47   4   150 (39.27)  1394  265 (40.90)
 4    206 100896    266 (  0.26)     6  0    0  47   8   1    56 (27.18)  1450  115 (43.23)
 0     60 100956     60 (  0.06)     0  0   45   0  13   1    59 (98.33)  1509   59 (98.33)
-1   4780 105736      0 (  0.00)  13784  0   130 743 196  26   1095 (22.91)  2604    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     202      202        3
  7       1      203        4
  8       4      207        5
  9       5      212        6
 10       5      217        7
 11       1      218        7
 12       2      220        9
 13       9      229        9
 14       1      230       10
 15       4      234       12
 16       9      243       16
 17       5      248       18
 18       4      252       21
 19       7      259       21
 20       7      266       21
 21       4      270       21
 22       6      276       19
 23       8      284       17
 24       5      289       17
 25       5      294       17
 26       5      299       16
 27       6      305       15
 28       8      313       17
 29       9      322       18
 30       9      331       17
 31       5      336       17
 32       7      343       18
 33      12      355       18
 34       4      359       17
 35       9      368       19
 37      12      380       17
 38       5      385       17
 39       5      390       18
 40      24      414       18
 42      13      427       16
 43      11      438       20
 44      13      451       21
 45      25      476       24
 46       8      484       24
 47       3      487       25
 48       3      490       25
 49       2      492       25
 50      16      508       28
 51     144      652       43
 52      32      684       51
 53      14      698       50
 54      36      734       56
 55      27      761       62
 56     292     1053       44
 57      10     1063       46
 58       9     1072       43
 59       2     1074       43
 60      62     1136       51
 61     104     1240       56
 65       1     1241       56
 66    1024     2265       15
 71       2     2267       16
 72       3     2270       17
 73       3     2273       18
 74       9     2282       21
 75      21     2303       29
 76      23     2326       31
 77      19     2345       33
 78       8     2353       31
 79      16     2369       28
 80       5     2374       28
 81     125     2499       45
 82      23     2522       45
 83      23     2545       51
 84      24     2569       54
 85      26     2595       47
 86      13     2608       41
 87      27     2635       43
 88      19     2654       38
 89      14     2668       37
 90    4349     7017        1

SS region: 1441 (20.54%), flagged: 1 (0.01%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
  663     -3.3  [-3.3,  0.0]  (1, 0)
 2210     -3.2  [-3.2,  0.0]  (1, 0)
 2555     -4.5  [-2.4,  0.0]  (2, 0)
 3622     -5.1  [-5.1,  0.0]  (0, 1)
 3656     -4.0  [-4.0,  0.0]  (1, 0)
 4073     -3.7  [-3.7,  0.0]  (0, 1)
 4514     -5.1  [-5.1,  0.0]  (0, 1)
 4579     -5.1  [-5.1,  0.0]  (0, 1)
 4803     -4.0  [-4.0,  0.0]  (0, 1)
 4874     -4.7  [-2.9,  0.0]  (2, 0)
 4939     -6.4  [-2.6,  0.0]  (3, 0)
 5461     -3.2  [-3.2,  0.0]  (0, 1)
 5527     -4.6  [-4.6,  0.0]  (0, 1)
 5597     -4.6  [-4.6,  0.0]  (0, 1)
 6192     -4.0  [-4.0,  0.0]  (0, 1)
 6197     -4.1  [-2.3,  0.0]  (0, 2)
 6240     -5.1  [-5.1,  0.0]  (0, 1)
 6483     -4.0  [-4.0,  0.0]  (0, 1)
 6861     -3.3  [-3.3,  0.0]  (1, 0)
 6946     -4.6  [-4.6,  0.0]  (0, 1)

Read/contig discrepancies (* = higher-quality):
   926  S     ag020109r1      (53)/(53)  925 TAT / TGT
   995  S     ag020109r1      (9)/(9)  991 AATTAC / AGTGGC
   998  I     ag020109r1      (0)/(0)  998 TA / TTA
  1007  I     ag020109r1      (0)/(0)  1007 AC / ACC
  1014  S     ag020109r1      (0)/(0)  1012 ATTC / AGGC
*  942  D   C ag020109f1      (95)/(72)  936 ATTAGCCT / ATATAT
  1027  S   C ag020109f1      (0)/(0)  1026 CNC / CNC
  1047  S   C ag020109f1      (0)/(0)  1046 TNC / TNC
  1071  S   C ag020109f1      (0)/(0)  1069 CNNT / CNNT
  1082  S   C ag020109f1      (0)/(0)  1077 TNCTNNT / TNCTNNT
  1091  S   C ag020109f1      (0)/(0)  1090 CNT / CNT
  1096  S   C ag020109f1      (0)/(0)  1095 CNC / CNC
  1174  S   C ag020109f1      (0)/(0)  1173 CNC / CNC
  1181  S   C ag020109f1      (0)/(0)  1177 ANNCNC / ANNCNC

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:

(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
(49, 0)  1118- 1136 [ 0.0] (0,71)   C ab030109f1         100-82 | 11 149 | LU:(11 70)(**112 149**) || local(+/-) (0.0,0.0), distant (0.0,0.0)
(0, 0)  1109- 1148 [ 0.7] (61,61)     ab030109r1         87-126 | 51 187 | LU:(51 86)(**127 187**) || local(+/-) (0.0,0.0), distant (0.0,0.0)
(78, 78)  1198- 2077 [17.7] (0,0)     bb080109f1         105-991 | 27 991 | LU:(**55 104**) || local(+/-) (13.5,9.4), distant (0.0,0.0)
(92, 109)  1269- 1751 [ 0.0] (0,0)     ae010109f1         137-619 | 28 619 | LU:(**28 62**) || local(+/-) (9.4,0.0), distant (0.0,0.0)
(0, 0)  1941- 2449 [ 9.0] (117,0)     bd090109f1         27-533 || local(+/-) (10.9,0.0), distant (0.0,0.0)
(0, 0)  6218- 6793 [-52.3] (310,0)   C ab070109r1         967-391 || local(+/-) (12.7,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -0.2 (<20 part: -0.2 (#=3), >20:0.0 (#=0); in HQ: 0.0, out HQ -0.2), match: 12.8  trail: -64.9  lead: 0.0  total: -52.3 
(0, 0)  6249- 7017 [12.3] (0,34)     ac120109f1         27-802 | 27 836 | LU:(803 836) || local(+/-) (14.4,9.8), distant (0.0,0.0)

Gaps in unique-read coverage:   I 991- 1120, I 1150- 1197, E 7019- 7051

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):