Hi all-
Apologies if this information has been posted elsewhere - I wasn't able to find what I was looking for searching the forums.
I'm using MAQ cns2SNP (and SNPfilter) to call SNPs on short read alignments, mouse genome. Though things have been going well, I'm having a hard time interpreting some of the output.
The MAQ manual states, for cns2SNP output:
"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. "
I'm having trouble interpreting "the average number of hits of reads covering this position." Can anyone translate this into something more well-defined?
Also, for "Phred-like consensus quality" - though I realize this is not a true Phred score, what is the best way to think about this? Overall consensus base quality at a given position? "Confidence score" for calling a SNP?
In general, using SNPfilter and some arbitrary filters (discussed on the forums), I've been ignoring called SNPs with a "Phred-like" score of <40. I'd like to know what this actually means and whether it makes good sense.
Thanks for you help!
Apologies if this information has been posted elsewhere - I wasn't able to find what I was looking for searching the forums.
I'm using MAQ cns2SNP (and SNPfilter) to call SNPs on short read alignments, mouse genome. Though things have been going well, I'm having a hard time interpreting some of the output.
The MAQ manual states, for cns2SNP output:
"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. "
I'm having trouble interpreting "the average number of hits of reads covering this position." Can anyone translate this into something more well-defined?
Also, for "Phred-like consensus quality" - though I realize this is not a true Phred score, what is the best way to think about this? Overall consensus base quality at a given position? "Confidence score" for calling a SNP?
In general, using SNPfilter and some arbitrary filters (discussed on the forums), I've been ignoring called SNPs with a "Phred-like" score of <40. I'd like to know what this actually means and whether it makes good sense.
Thanks for you help!
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