details: http://www.bx.psu.edu/hg/galaxy/rev/5d5e5da2fcda changeset: 3242:5d5e5da2fcda user: Anton Nekrutenko <anton@bx.psu.edu> date: Thu Jan 14 14:20:01 2010 -0500 description: Small edit for the help section diffstat: tools/samtools/pileup_parser.xml | 6 +++--- 1 files changed, 3 insertions(+), 3 deletions(-) diffs (16 lines): diff -r ec77ae7f9b4f -r 5d5e5da2fcda tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml Thu Jan 14 14:13:42 2010 -0500 +++ b/tools/samtools/pileup_parser.xml Thu Jan 14 14:20:01 2010 -0500 @@ -272,9 +272,9 @@ will report everything from the original file:: - chrM 412 A 2 ., II 0 0 0 0 2 - chrM 413 G 4 ..t, III2 0 0 0 1 3 - chrM 414 C 4 ...a III2 0 0 0 0 3 + chrM 412 A 2 ., II 2 0 0 0 2 + chrM 413 G 4 ..t, III2 0 0 2 1 3 + chrM 414 C 4 ...a III2 3 0 0 0 3 chrM 415 C 4 TTTt III7 0 0 0 4 4 Here, you can see that although the total coverage at position 414 is 4 (column 4), the quality adjusted coverage is 3 (last column). This is because only three out of four reads have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion, 40, 40, 40, 17).