This file provides a decription of the columns found in the chromosome reports.

rsNumber:  The integer that follows rs for the SNP record.

snpAlleles:  The alleles that are reported as having been observed for the SNP

matchIndex: Total number of matches (totalMatches) are the number of times a SNP can be mapped to a position in the genome at at least 95% identity in a high scoring pair that spans at least 90% of the supplied context sequence.  The match index indicates the rank of the identity for this position.  Therefore, the best match will always be matchIndex=1, the least quality match would have matchIndex=totalMatches

totalMatches:  See matchIndex

chrName: The name for the chromosome for this match	

chrPos: The 1 indexed position to which the SNP maps.	

Orientation:  The orientation of the SNP context to the chromosome (f/r)	

chrAllele:  The allele present on the reference sequence at the position to which the SNP maps.	

Discrepancy:  An indication as to whether or not the reference allele is consistent with the reported alleles for the SNP

mismatch3: Was there a gap in the three bases either upstream of downstream of the SNP.  This affects the positioning of the SNP.

The next four columns are the allele counts across all matches with greater than 95% identity in a high scoring pair that spans at least 90% of the supplied context sequence

example

A	C	G	T	#explanation	
1	0	0	0	#total matches = 1, and an A was found at that position
0	1	1	0	#total matches = 2, and an C and a G were found at those positions
0	3	0	1	#total matches = 4, and 3 Cs and a T were found at those positions


The next four columns are identical to those above except that they are for all matches with greater than 94.1% identity within the (up to) 25 bases that flank the SNP on each side. 

A   C	 G    T
1   0	 0    0	#hits = 1, and an A was found at that position
0   8	 4    0	#hits = 12, and 8 Cs and 4 T were found at those positions