The location of Pepper Chip assembly unigenes sequences in the pepper CM334 (v1.5) (KIM et al. 2014), pepper Zunla-1 (release 2.0) (QIN et al. 2014),
tomato (SL2.50, http://solgenomics.net/organism/1/genome ) (FERNANDEZ-POZO et al. 2015)and potato (Stuberosum_206_v3.4,
http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organi sm=Stuberosum) (GRIGORIEV et al. 2012) genome assemblies were determined using
GMAP with default settings (WU and WATANABE 2005).

These files contain the unfiltered GMAP output in BLAT format:

PepperChipAssembly_Vs_Pepper_Genome_Qin_Zunla_v2.BLAT
PepperChipAssembly_Vs_Pepper_Genome_V1_5.BLAT
PepperChipAssembly_Vs_Potato_Genome_V_2_6_0.BLAT
PepperChipAssembly_Vs_toamto_Genome_2_5.BLAT

Column Headers for BLAT files:
1.	matches - Number of matching bases that aren't repeats.
2.	misMatches - Number of bases that don't match.
3.	repMatches - Number of matching bases that are part of repeats.
4.	nCount - Number of 'N' bases.
5.	qNumInsert - Number of inserts in query.
6.	qBaseInsert - Number of bases inserted into query.
7.	tNumInsert - Number of inserts in target.
8.	tBaseInsert - Number of bases inserted into target.
9.	strand - defined as + (forward) or - (reverse) for query strand. In mouse, a second '+' or '-' indecates genomic strand.
10.	qName - Query sequence name.
11.	qSize - Query sequence size.
12.	qStart - Alignment start position in query.
13.	qEnd - Alignment end position in query.
14.	tName - Target sequence name.
15.	tSize - Target sequence size.
16.	tStart - Alignment start position in query.
17.	tEnd - Alignment end position in query.
18.	blockCount - Number of blocks in the alignment.
19.	blockSizes - Comma-separated list of sizes of each block.
20.	qStarts - Comma-separated list of start position of each block in query.
21.	tStarts - Comma-separated list of start position of each block in target.

Physical and FA07 v6 and NM06 v3 genetic posistions of Pepper Chip unigenes with unique matches to each of the genomes. 

The BLAT output files were filtered to select high confidence hits. The pepper CM334 v1.5 and Zunla-1 v2 genome matches were filtered at 98%
identity, minimum alignment length of 200 nucleotides (nt) and a maximum of 50 unaligned nt at either end of the unigene. If there were multiple hits
with the same score for a given EST after filtering, the position of the EST in the genome was considered ambiguous and dropped. The tomato and
potato genome hits were filtered at minimums of 80% identity and 75% coverage with a minimum length of 200 nt. When there were multiple hits for a
given EST, the hit with highest identity and coverage was retained. If there was no single hit with both highest identity and coverage, the unigene
was removed.

Column definitions:
qName	 Query sequence name, GMAP
tName	 Target sequence name, GMAP
tChr	 Target chromosome or type (chromosome or scaffold)
tChr#	 Target chromosome number
tStart	 Alignment start position in target
tEnd	 Alignment end position in target
tSize	 Target sequence size
qSize	 Query sequence size
Aln_length	Number of aligned nucleotides between query and target
%Query_Coverage	Percent of nucleotides in query sequence aligned to target	
%_Identity	The percentage of aligned sequences that were perfect matches
NM06_LG		NM06 linkage group number based on pepper chromosome number.	
NM06_Pos(cM)	Position in cM on the NM06 linkage group (linkage groups oriented based on the Wu et al., 2009 pepper COSII map).
FA07_LG		FA07 map linkage group number based on pepper chromosome number.
FA07_Pos(cM)	Position in cM on the FA07 linkage group (linkage groups oriented based on the Wu et al., 2009 pepper COSII map).


