[maq-help] SNP Report Columns and Qualities

[shaffer <sh...@ch...>]

Hi,
I've seen another mention on this list about the 7th column  
description (for the cns2snp output) in the manual being labeled as  
the 8th column.  Heng responded that it was just an old version of the  
manual, and the newest is corrected.  The main site links to the  
manual here: http://maq.sourceforge.net/maq-manpage.shtml but this  
version still seems to have the error (second word, fourth full  
paragraph in the "cns2snp" section).  Is there a new(er) manual out  
there somewhere?

Also, after reading the FAQ/manual/mail-list, I haven't been able to  
discover why the "consensus quality" scores in the 5th column seem to  
range from 1-255.  Shouldn't "phred-like" quality scores be in the  
range of 1-40?  If not, what's a "good" threshold in this larger  
range, and why?

It seems the read depth (6th col?) also has a max value of 255, which  
also confused me a little.

Anyway, here is a small sample from my cns.filtered.snp report that  
I'm seeing:

mm8_dna 9463    G       C       255     255     1.00    63       
62      Y       171     T
mm8_dna 14663   G       A       206     189     1.00    63       
62      T       255     W
mm8_dna 32182   C       G       255     255     1.00    63       
62      K       208     T
mm8_dna 32360   C       T       255     255     1.00    63       
62      Y       67      C
mm8_dna 32455   T       G       255     255     1.00    63       
62      T       115     K
mm8_dna 32523   C       A       255     255     1.00    63       
62      G       76      R
mm8_dna 32588   A       G       255     255     1.00    63       
62      K       79      T
mm8_dna 32661   G       A       255     255     1.00    63       
62      W       213     T
mm8_dna 32962   T       C       255     255     1.00    63       
62      M       219     A
mm8_dna 33100   C       T       243     187     1.00    63       
62      N       255     N
mm8_dna 33101   A       G       177     158     1.00    63       
62      T       225     K
mm8_dna 33459   C       T       255     255     1.00    63       
62      Y       187     C

Thanks in advance for any clarification,
Christian