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  • maq output

    hello,
    Apologies if this has been asked before. one of output in MAQ is cns.snp. it looks like:
    dsm1731_genome 2719519 T W 16 24 1.00 63 20 T 122 A
    in manual of MAQ, it describe as:
    "Each line consists of chromosome, position, reference base, consensus base, Phred-like consensus quality, read depth, the average number of hits of reads covering this position, the highest mapping quality of the reads covering the position, the minimum consensus quality in the 3bp flanking regions at each side of the site (6bp in total), the second best call, log likelihood ratio of the second best and the third best call, and the third best call."
    and "The 8th column roughly gives the copy number of the flanking region in the reference genome. In most cases, this number approaches 1.00, which means the region is about unique."
    my question is the 7th column of my result is 1.00, but the manual describe the 8th column "In most cases, this number approaches 1.00". why?
    thanks.

  • #2
    the manual is outdated. MAQ itself is not being actively updated anymore.
    --
    bioinfosm

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