The samtools unix man page describes the mpileup output format
quite adequately. "... At the read base column, a symbol '^'
marks the start of a read. The ASCII of the character following
'^' minus 33 gives the mapping quality. A symbol '$' marks the
end of a read segment."
- tom blackwell -
On Tue, 3 Nov 2015, ???? wrote:
Dear Thomas,
Sorry to bother you again. I used this command
"/software/biosoft/software/samtools-1.0/samtools mpileup -A -B -d 999999999 -Q 0 -f
ref.fa filter_chr06_crick.sort.bam > filter_chr06_crick.sort.bam.pile" to generate a
pileup format file.
However, the read bases for the 2nd line are "^.,", then why the number of reads covering the site is
"1"? What does "F" mean in the 9th line? What does "0" mean in the 10th line? It is
highly appreciated if you could let us know the reason. Thanks so much!
Followings are some lines from file "filter_chr06_crick.sort.bam.pile":
1 chr06 19482560 G 1 a$ <
2 chr06 19539155 g 1 ^., F
3 chr06 19539156 t 1 , F
4 chr06 19539157 t 1 , B
5 chr06 19539158 g 1 a B
6 chr06 19539159 c 1 , 0
7 chr06 19539160 t 1 , F
8 chr06 19539161 a 1 , F
9 chr06 19656072 a 1 ^F, B
10 chr06 19682319 t 1 ^0, I
Followings are 3 lines from file "filter_chr06_crick.sort.bam":
SRR1026165.3918 16 chr06 19482466 37 95M * 0 0
AAAATACCCTCCATAAATAACACATAACGATTTTCATTATTTTTACATCCAAAAAATATAATTTTTACTTACATTATATTCAACTATATTCCTTA
FFFB<<BB<B<<FFFFFFFFFFFIFFBBIIIIFFBIIIIIIIFFIFIIFFIIIIIIIIIFFIIIFFFFIFFFIIFIIFFFFFFFFFFFFFBFF<<
XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:95
SRR1026165.2053 16 chr06 19539155 13 92M * 0 0
GTTACTAATAAATAACTAAAACTTCGCCAACTTACTATTCCGCCTTCACGATTAACCTACTATACAAACGCTGATAAACGTCTTCGTCATTA
FFBB0FFFFFFFFBB7<FFB<BFBB<7'BBBFFFFFFFFBBFFFFFFBBIIFFFFFFFFFIIIFFIFFFFFIFIIIFFBFFBFFBFFBFBBB
XT:A:U NM:i:0 X0:i:1 X1:i:11 XM:i:0 XO:i:0 XG:i:0 MD:Z:92
SRR1026165.7615 16 chr06 19656072 37 96M * 0
0
ATTTAAAAATATTATTTAAAATTTTAAAATTCAATTTTTTAATTAATAAAACAAAATCACCAAAAAAAATAATCAAAATAATAACAAAAAAAACAC
BFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBFFFFFFFFFFFFFFFFFFFBFFFFFFFFFIIIIIIIIIIIFFIIIIIIIIIFFFFFFFFFFBBB
XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:96
--
Fang Liang,
Beijing Institute of Genomics
Chinese Academy of Sciences
Tel +86(010)84097638------------------------------------------------------------------------------
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