I have a pileup from samtools (an mpileup too, but they agree with each other) that shows very odd quality scores. My fastq and .sam agree that the quality scores of the letters in the read range from B to h, which is normal.
The fastq and the .sam agree that the quality of the reads falling across a certain locus are quite high. But the quality scores of the pileup are strange. They range from ! to h, and certain positions are uniformly low, sometimes extremely so.
Here's a sample: The mixed SNP are 4107 looks awful based on the pileup, but going back to the original reads, the quality is great for C's and A's in that position. When I use an older version of samtools (0.1.7) on the same .bam, the pileup qualities are correct. When I use pileup in 0.1.12a, it looks like it does below, and the qualities are wrong.
chr2 69574093 G G 111 0 36 28 .,...,.,..,.,,..,.,,.,,..,.. QhhfchhhhhhhhhhahhghhhhhehNN
chr2 69574094 A A 111 0 36 28 .,...,.,..,.,,..,.,,.,,..,.. OhhgShhhhhhfhhc]fgghhhhfehNN
chr2 69574095 G G 111 0 36 28 .,...,.,..,.,,..,.,,.,,..,.. NhhgahhhhhhhhhhbhhghhhhhchOO
chr2 69574096 A A 111 0 36 28 .,...,.,..,.,,..,.,,.,,..,.. NhhfWhhhghhhhhh`hhgghhhhfhQQ
chr2 69574097 G G 114 0 36 29 .$,...,.,..,.,,..,.,,.,,..,..^F. DhhgahhhhhhhehhadhghhhhhahRRD
chr2 69574098 A A 111 0 36 28 ,...,.,..,.,,..,.,,.,,..,... hhdYhhhghhhehhahgghhhggchUUI
chr2 69574099 T T 111 0 36 28 ,...,.,..,.,,..,.,,.,,..,... aaaaaaaaaaaaaaaaaaaaaaaaaaa_
chr2 69574100 T T 114 0 36 29 ,...,.,..,.,,..,.,,.,,..,...^F, _aaaaaaaaaaaaaaaaaaaaaaaaaaaE
chr2 69574101 G G 117 0 36 30 ,...,.,..,.,,..,.,,.,,..,...,^F, UhgchhhhhhhehhcchfhhhhhfhhhgUE
chr2 69574102 A A 123 0 36 32 ,$...,.,..,.,,..,.,,.,,..,...,,^F.^:, >EMY\\O\\\O5OPPPO\O\\POP\OS\\U?@
chr2 69574103 A A 120 0 36 31 ...,.,..,.,,..,.,,.,,..,...,,., BJZZZLZZZL2LMMMLZLZZMLMZLPZZ[AA
chr2 69574104 A A 103 0 36 31 ...,.,..,.c,..,.,,.,,..,...,,., AFZZZJZZZK0KKKKKZKZZKKKZKNZZ[BB
chr2 69574105 A A 120 0 36 32 .$..,.,..,.,,..,.,,.,,..,...,,.,^:. ?:\\\?\\\@5@@@@@\@\\@@@\@D\\]E?#
chr2 69574106 C C 75 0 37 33 ..,.,..,.,,..,.,,.,,..,...,,.,.^:.^F, %^^a!aaa!J!!!!!a!aa!!!a!'aaaa!#!B
chr2 69574107 C C 78 0 37 35 A$.,.a..,A,aAAaA,a.,aAA,AA.,,.aAA,^F.^:a !UUa!aaa!\!!!!!`!aa!!!a!%aaaa!!!EE!
chr2 69574108 A A 78 0 37 34 .$,$.,..,.,,..,.,,.,,..,...,,.,..,., CCU!ehh!h!!!!!Z!hh!!!h!'ghhh!!$cU!
chr2 69574109 G G 123 0 35 32 .,..,.,,..,.,,.,,..,...,,.,..,., R4bhhPhPPPPPgPhhQPQhPTghhhQGPhe?
chr2 69574110 A A 123 0 35 32 .$,$..,.,,..,.,,.,,..,...,,.,..,., >4>\\P\PPPPP\P\\QPP\PT\\\\PPR\\A
chr2 69574111 A A 117 0 35 30 .$.,.,,..,.,,.,,..,...,,.,..,., ;ZZVZVVVVVZVZZWVWZVXZZZZWUYZZD
chr2 69574112 A A 114 0 35 29 .,.,,..,.,,.,,..,...,,.,..,., YYYZYYYYYZYZZYYYZYZZZZZYYYZZO
chr2 69574113 A A 117 0 35 30 .,.,,..,.,,.,,..,...,,.,..,.,^F. TT\\\\\\\\\\\\\\\\\\\\\\\\\\SE
chr2 69574114 C C 117 0 35 30 .,.,,..,.,,.,,..,...,,.,..,.,. RRhhhhgghghhhahZghhchhhfhhhhhR
chr2 69574115 A A 117 0 35 30 .$,$.,,..,.,,.,,..,...,,.,..,.,. DDhhhhghgahhhgeVhhhghhhfhhghhU
chr2 69574116 G G 114 0 35 29 .,,..,.,,.,,..,...,,.,..,.,.^F. hhbh`fhghhhhhOhfhghhgahhhhhhE
chr2 69574117 A A 117 0 35 30 .,,..,.,,.,,..,...,,.,..,.,..^:, ah_cchhghhhdgThghghhhdhhhhhhU@
chr2 69574118 T T 111 0 35 30 .,,..,.,,.,,.C,...,,.,..,.,.., Bh2PQQQgQhgQ+-hQQahhhVQQhhQhbB
chr2 69574119 G G 114 0 35 31 .,,..,.,,.,,..,...,,.,..,.,..,^F. 0e/LMMMgMghM'-hMMghhhRMMfhMheAB
chr2 69574120 C C 72 0 37 32 .,,..,.,,.,,..,...,,.,..,.,..,.^F. ,E+!!!!a!aa!$+a!!aaaa'!!aa!aa!BB
chr2 69574121 C C 75 0 37 33 T$,$tTTtT,t.,tTT,TT.,,.tTT,.t..t..^F. !A!!!!!a!aa!!+a!!aaaa'!!aa!aa!BEE
chr2 69574122 G G 117 0 35 32 ,$..,.,,.,,..,...,,.,..,.,..,...^:. !;<;;g;hh;!0h;;ahhh@;;gh;hh;BbRE
chr2 69574123 C C 117 0 35 31 ..,.,,.,,..,...,,.,..,.,..,.... ;<;;g;hh;!2h;;dggh@;;hh;hh;BeUQ
chr2 69574124 T T 120 0 34 32 ..,.,,.,,C.,...,,.,..,.,..,....^:. AQQQgQhhQ!7hQQdhhhVQQhhQhhPBgheE
chr2 69574125 A A 126 0 34 33 .$.,.,,.,,..,...,,.,..,.,..,.....^:. @dhhfhghfNahhfdghhdhhhhhhhhBeghUE
The fastq and the .sam agree that the quality of the reads falling across a certain locus are quite high. But the quality scores of the pileup are strange. They range from ! to h, and certain positions are uniformly low, sometimes extremely so.
Here's a sample: The mixed SNP are 4107 looks awful based on the pileup, but going back to the original reads, the quality is great for C's and A's in that position. When I use an older version of samtools (0.1.7) on the same .bam, the pileup qualities are correct. When I use pileup in 0.1.12a, it looks like it does below, and the qualities are wrong.
chr2 69574093 G G 111 0 36 28 .,...,.,..,.,,..,.,,.,,..,.. QhhfchhhhhhhhhhahhghhhhhehNN
chr2 69574094 A A 111 0 36 28 .,...,.,..,.,,..,.,,.,,..,.. OhhgShhhhhhfhhc]fgghhhhfehNN
chr2 69574095 G G 111 0 36 28 .,...,.,..,.,,..,.,,.,,..,.. NhhgahhhhhhhhhhbhhghhhhhchOO
chr2 69574096 A A 111 0 36 28 .,...,.,..,.,,..,.,,.,,..,.. NhhfWhhhghhhhhh`hhgghhhhfhQQ
chr2 69574097 G G 114 0 36 29 .$,...,.,..,.,,..,.,,.,,..,..^F. DhhgahhhhhhhehhadhghhhhhahRRD
chr2 69574098 A A 111 0 36 28 ,...,.,..,.,,..,.,,.,,..,... hhdYhhhghhhehhahgghhhggchUUI
chr2 69574099 T T 111 0 36 28 ,...,.,..,.,,..,.,,.,,..,... aaaaaaaaaaaaaaaaaaaaaaaaaaa_
chr2 69574100 T T 114 0 36 29 ,...,.,..,.,,..,.,,.,,..,...^F, _aaaaaaaaaaaaaaaaaaaaaaaaaaaE
chr2 69574101 G G 117 0 36 30 ,...,.,..,.,,..,.,,.,,..,...,^F, UhgchhhhhhhehhcchfhhhhhfhhhgUE
chr2 69574102 A A 123 0 36 32 ,$...,.,..,.,,..,.,,.,,..,...,,^F.^:, >EMY\\O\\\O5OPPPO\O\\POP\OS\\U?@
chr2 69574103 A A 120 0 36 31 ...,.,..,.,,..,.,,.,,..,...,,., BJZZZLZZZL2LMMMLZLZZMLMZLPZZ[AA
chr2 69574104 A A 103 0 36 31 ...,.,..,.c,..,.,,.,,..,...,,., AFZZZJZZZK0KKKKKZKZZKKKZKNZZ[BB
chr2 69574105 A A 120 0 36 32 .$..,.,..,.,,..,.,,.,,..,...,,.,^:. ?:\\\?\\\@5@@@@@\@\\@@@\@D\\]E?#
chr2 69574106 C C 75 0 37 33 ..,.,..,.,,..,.,,.,,..,...,,.,.^:.^F, %^^a!aaa!J!!!!!a!aa!!!a!'aaaa!#!B
chr2 69574107 C C 78 0 37 35 A$.,.a..,A,aAAaA,a.,aAA,AA.,,.aAA,^F.^:a !UUa!aaa!\!!!!!`!aa!!!a!%aaaa!!!EE!
chr2 69574108 A A 78 0 37 34 .$,$.,..,.,,..,.,,.,,..,...,,.,..,., CCU!ehh!h!!!!!Z!hh!!!h!'ghhh!!$cU!
chr2 69574109 G G 123 0 35 32 .,..,.,,..,.,,.,,..,...,,.,..,., R4bhhPhPPPPPgPhhQPQhPTghhhQGPhe?
chr2 69574110 A A 123 0 35 32 .$,$..,.,,..,.,,.,,..,...,,.,..,., >4>\\P\PPPPP\P\\QPP\PT\\\\PPR\\A
chr2 69574111 A A 117 0 35 30 .$.,.,,..,.,,.,,..,...,,.,..,., ;ZZVZVVVVVZVZZWVWZVXZZZZWUYZZD
chr2 69574112 A A 114 0 35 29 .,.,,..,.,,.,,..,...,,.,..,., YYYZYYYYYZYZZYYYZYZZZZZYYYZZO
chr2 69574113 A A 117 0 35 30 .,.,,..,.,,.,,..,...,,.,..,.,^F. TT\\\\\\\\\\\\\\\\\\\\\\\\\\SE
chr2 69574114 C C 117 0 35 30 .,.,,..,.,,.,,..,...,,.,..,.,. RRhhhhgghghhhahZghhchhhfhhhhhR
chr2 69574115 A A 117 0 35 30 .$,$.,,..,.,,.,,..,...,,.,..,.,. DDhhhhghgahhhgeVhhhghhhfhhghhU
chr2 69574116 G G 114 0 35 29 .,,..,.,,.,,..,...,,.,..,.,.^F. hhbh`fhghhhhhOhfhghhgahhhhhhE
chr2 69574117 A A 117 0 35 30 .,,..,.,,.,,..,...,,.,..,.,..^:, ah_cchhghhhdgThghghhhdhhhhhhU@
chr2 69574118 T T 111 0 35 30 .,,..,.,,.,,.C,...,,.,..,.,.., Bh2PQQQgQhgQ+-hQQahhhVQQhhQhbB
chr2 69574119 G G 114 0 35 31 .,,..,.,,.,,..,...,,.,..,.,..,^F. 0e/LMMMgMghM'-hMMghhhRMMfhMheAB
chr2 69574120 C C 72 0 37 32 .,,..,.,,.,,..,...,,.,..,.,..,.^F. ,E+!!!!a!aa!$+a!!aaaa'!!aa!aa!BB
chr2 69574121 C C 75 0 37 33 T$,$tTTtT,t.,tTT,TT.,,.tTT,.t..t..^F. !A!!!!!a!aa!!+a!!aaaa'!!aa!aa!BEE
chr2 69574122 G G 117 0 35 32 ,$..,.,,.,,..,...,,.,..,.,..,...^:. !;<;;g;hh;!0h;;ahhh@;;gh;hh;BbRE
chr2 69574123 C C 117 0 35 31 ..,.,,.,,..,...,,.,..,.,..,.... ;<;;g;hh;!2h;;dggh@;;hh;hh;BeUQ
chr2 69574124 T T 120 0 34 32 ..,.,,.,,C.,...,,.,..,.,..,....^:. AQQQgQhhQ!7hQQdhhhVQQhhQhhPBgheE
chr2 69574125 A A 126 0 34 33 .$.,.,,.,,..,...,,.,..,.,..,.....^:. @dhhfhghfNahhfdghhdhhhhhhhhBeghUE
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