samtools: understanding a same SNP from different samples

drio

Senior Member

Join Date: Oct 2008
Posts: 323

samtools: understanding a same SNP from different samples

03-02-2010, 01:01 PM

Code:

722:
chr18   23839852        
T       W       81      81      60	57     
 .$.......,..............a.a.a,a,.a.aa.,.a.a.,.a.a,,.,.,.a.      :^`_^]``8```````[``````A`O`="H"`@ZLM`"`=`RW`YO`J5"`"`"`M`
718:
chr18   23839852        
T       W       12      12      60      29      
.$............aa,.a,.a.a,,,a.,  <`J`````O`O``N9"[8"`6`:6`"8`4
722:
chr18   23839852        
T       W       13      13      60      59      
.$.........,.a............,,.,a.,.,.a..a.a.,a..,.a.,aa.,,.aa    ?N`]`[````#Y5`\\``F``````"%`&?`>`>`@``G`@^)F`=``E`":=I""`DB

I see a clear indication of SNP in any of those cases but the last two ones have much smaller phred scores than the first one. I am trying to figure out why is that. Comments?

-drd

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