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Old 06-06-2011, 11:02 AM   #1
HMorrison
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Location: Massachusetts

Join Date: May 2009
Posts: 116
Default MAQ cns.snp output

Hi, I am learning to use MAQ; have the most recent version, and get reasonable looking output, but the manual and reference pages describe the columns 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."

These column descriptions do not seem to match the current snp table. For example, my 8th column has values of 63, but the description says "The 8th column roughly gives the copy number of the flanking region in the reference genome. In most cases, this number approaches 1.00..."

Can anyone direct me to current documentation? There are no documents in the /maq directory itself.
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