What it does

This tool maps SOLiD color-space reads against the target genome using MAQ. It produces three output datasets:

ALIGNMENT INFO : contains the read alignment information,

PILEUP : contains the coverage and SNP statistics for every nucleotide of the target genome,

CUSTOM TRACK : contains the coverage and SNP statistics as custom tracks displayable in the UCSC browser.

The ALIGNMENT INFO dataset will contain the following fields:

• column 1 = read name
• column 2 = chromosome
• column 3 = position
• column 4 = strand
• column 5 = insert size from the outer coorniates of a pair
• column 6 = paired flag
• column 7 = mapping quality
• column 8 = single-end mapping quality
• column 9 = alternative mapping quality
• column 10 = number of mismatches of the best hit
• column 11 = sum of qualities of mismatched bases of the best hit
• column 12 = number of 0-mismatch hits of the first 24bp
• column 13 = number of 1-mismatch hits of the first 24bp on the reference
• column 14 = length of the read
• column 15 = read sequence
• column 16 = read quality

The PILEUP dataset will contain the following fields:

• column 1 = chromosome
• column 2 = position
• column 3 = reference nucleotide
• column 4 = coverage (number of reads that cover this position)
• column 5 = number of SNPs
• column 6 = number of As
• column 7 = number of Ts
• column 8 = number of Gs
• column 9 = number of Cs