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SORRY, it was caused by an command error. Please neglect
I postd this on a reply to another thread but thought it is weird enough to become a new thread. ~50% (~32000) of snp calls were "N"s and the rest being ATCG or IUCAC codes. But the large proportion of Ns with decent quality is just weird. Am I doing something very wrong or what? Please see below and tap in your thoughts.
Don't understand the following records from pileup -C 50 -vcf (samtools 0.1.12a):
Why is the consensus N when the SNP quality and MappingQ all seem pretty good?
Thanks!
CSoong
chr1 808922 G N 125 225 28 50 AAAAAaaAAaaaaaAAAAAAaaAaAAAAaAAAA..aaAaaAAAAAaaaaa &><<<<;::@;;89<>=<;;;:;.9:;:9;<=;+A8;;88;>;;98: 9/.
chr1 808928 C N 134 221 30 57 TTTttTTtttttTTTTTTttTtTTTTtTTTT..ttTttTTTTTttttttT ttttTTT 98=<;89=;?;<;8>;8:;=88?988<:899FH;=8;;9:?99==;;?.: <:7=::!
chr1 809681 G N 99 99 44 82 ,$..,..,.,...,...,,,,,..,.....a.,a..AaAa,A,Aa.AAA. .aaa..A.A.a.,AAAA,A...A,..A.....^S. >88E?BFBHBB?HBBCHH=HH:9HAABBB81F9AA=8;;>;F;8B;?<%A ::9?B;B=A9BF;@;;B<@AA<D@@<@@?>=>
chr1 809687 G N 97 97 45 85 .,.,...,...,,,,,..,.....c.,c..CcCc,C,Cc.CCC..ccc.. C.C.c.,CCCC,C...C,..C........,C..^S,^S. IFGG>FJHIJIHH=HHFFHIFJHH><H?-H6?9?B9C<>J399%J?>?FI<H9?8JI;@;;H>AFI:IEE;HHHHGIHG F.FB?>
I postd this on a reply to another thread but thought it is weird enough to become a new thread. ~50% (~32000) of snp calls were "N"s and the rest being ATCG or IUCAC codes. But the large proportion of Ns with decent quality is just weird. Am I doing something very wrong or what? Please see below and tap in your thoughts.
Don't understand the following records from pileup -C 50 -vcf (samtools 0.1.12a):
Why is the consensus N when the SNP quality and MappingQ all seem pretty good?
Thanks!
CSoong
chr1 808922 G N 125 225 28 50 AAAAAaaAAaaaaaAAAAAAaaAaAAAAaAAAA..aaAaaAAAAAaaaaa &><<<<;::@;;89<>=<;;;:;.9:;:9;<=;+A8;;88;>;;98: 9/.
chr1 808928 C N 134 221 30 57 TTTttTTtttttTTTTTTttTtTTTTtTTTT..ttTttTTTTTttttttT ttttTTT 98=<;89=;?;<;8>;8:;=88?988<:899FH;=8;;9:?99==;;?.: <:7=::!
chr1 809681 G N 99 99 44 82 ,$..,..,.,...,...,,,,,..,.....a.,a..AaAa,A,Aa.AAA. .aaa..A.A.a.,AAAA,A...A,..A.....^S. >88E?BFBHBB?HBBCHH=HH:9HAABBB81F9AA=8;;>;F;8B;?<%A ::9?B;B=A9BF;@;;B<@AA<D@@<@@?>=>
chr1 809687 G N 97 97 45 85 .,.,...,...,,,,,..,.....c.,c..CcCc,C,Cc.CCC..ccc.. C.C.c.,CCCC,C...C,..C........,C..^S,^S. IFGG>FJHIJIHH=HHFFHIFJHH><H?-H6?9?B9C<>J399%J?>?FI<H9?8JI;@;;H>AFI:IEE;HHHHGIHG F.FB?>
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