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Old 03-04-2010, 12:21 AM   #1
zslee
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Default something i don't understand of samtools pileup result

chr10 856918 A W 109 109 60 15 ,...T,..t.,T,,, aaN`a_aa`_`_b__
the above is one line of my samtool pileup results, in this position, the reference base is A, so the reverse strand base should be T,
but in the bases column(9th column), there is one 't', which means a mismatch on reverse strand(but in fact it should be one match), how to explain this ? or a bug ?

i don't know whether i make the question clear, anyone can help me

thanks

ZSL
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Old 03-04-2010, 12:25 AM   #2
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Quote:
Originally Posted by zslee View Post
chr10 856918 A W 109 109 60 15 ,...T,..t.,T,,, aaN`a_aa`_`_b__
the above is one line of my samtool pileup results, in this position, the reference base is A, so the reverse strand base should be T,
but in the bases column(9th column), there is one 't', which means a mismatch on reverse strand(but in fact it should be one match), how to explain this ? or a bug ?

i don't know whether i make the question clear, anyone can help me

thanks

ZSL
The 9th column is always with respect to the "+" strand. So the lower case "t" means there is a mismatch on the "-" strand, when reverse complimented is "t". Therefore, the mismatch is an "a" with respect to the "-" strand. If you go back to your read data, you will find such a read (with an "a" mismatch).
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Old 03-04-2010, 12:29 AM   #3
zslee
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Quote:
Originally Posted by nilshomer View Post
The 9th column is always with respect to the "+" strand. So the lower case "t" means there is a mismatch on the "-" strand, when reverse complimented is "t". Therefore, the mismatch is an "a" with respect to the "-" strand. If you go back to your read data, you will find such a read (with an "a" mismatch).
OK, thanks a lot ! i understand now
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Old 12-20-2010, 03:01 PM   #4
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Hello everybody,

I also do no understand a part of my pileup output (alignment generated with novoalign sam), maybe this is straightforward for somebody around? I would be very grateful if anybody can help.

Is there a way to tell what is the "consensus" sequence according to the reads mapped here?

CTCAA A--TCT?

Contig1 4787 C C 60 0 60 11 ,,,,..,.... DAEC<=;>;;7
Contig1 4788 T T 60 0 60 11 ,,,,..,.... @:>;:;C@;?:
Contig1 4789 C C 60 0 60 11 ,,,,..,.... DAC=<??A;<9
Contig1 4790 A A 60 0 60 11 ,,,,..,.... ((()(((((((
Contig1 4791 A A 55 0 60 12 ,,,,..,....^~. %%%&%%%%%%%!
Contig1 4792 A N 0 0 0 12 ,,,,..,..... !!!!!!!!!!!!
Contig1 4793 A N 0 0 0 12 ,-1a,-1a,-1a,.-1A.-1A,-1a.-1A.-1A.-1A.-1A. !!!!!!!!!!!!
Contig1 4793 * -A/-A 74 399 60 12 -A * 10 2 0 0 0
Contig1 4794 A A 30 0 60 13 ***g-1t*******.^p, C?B!?A6?>B7!>
Contig1 4794 * -T/-T 37 77 60 13 -T * 1 12 0 0 0
Contig1 4795 T T 72 0 60 17 ,,,*..,....A,^l.^~.^~.^~. C?BB?A6?>B7!8;E<:
Contig1 4796 C C 81 0 60 18 ,,,,..,.....,....^~. F?CB@?>?;<8E<?;47=
Contig1 4797 T T 81 0 60 18 ,,,,..,.....,..... D>??AACB7@<>=DC;=<

Thanks a lot!
Yvan
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Old 12-21-2010, 01:53 AM   #5
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or maybe
CTCAAAA-TCT ?
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Old 12-21-2010, 11:04 AM   #6
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Looks like a single A deletion to me

You can check with

1) Velvet

2) Examine the reads themselves

3) realign the reads to a corrected genome, and see if they match with no discrepancies.
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Old 12-21-2010, 02:21 PM   #7
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Or you can try the pileup2fa that comes with samtools.pl
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Old 12-25-2010, 03:09 AM   #8
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THIS WAS CAUSED BY COMMAND LINE ERROR. SORRY. PLEASE NEGLECT!

a weird situation:

don't understand the following records from pileup -vcf -C 50 (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..ttTttTTTTTttttttTttttTTT 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;HHHHGIHGF.FB?>

Last edited by csoong; 12-25-2010 at 04:21 AM.
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Old 12-26-2010, 05:01 AM   #9
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How do the actual alignments on those locations look like (use samtools tview).
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Old 12-26-2010, 11:28 AM   #10
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Hi Drio,
it was a command line error. please neglect the post. I couldn't find a way to delete the post. Sorry about it.
CSoong
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Old 12-26-2010, 01:28 PM   #11
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Still wondering how you could get that consensus on those calls.
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Old 12-26-2010, 04:36 PM   #12
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since you asked, it's a result of an embarrassing awk command to collect 'N' in the pileup files.
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