On 21 Feb 2018, at 20:05, Nicholas Hill <nish...@ucsc.edu> wrote:
> Say my pileup line is this:
> chr3 73912 A 21 g,,..G,.gGGGgGGg,.Ggg JJ<JJJ<sJJssJJsss7JkJ
>
> So at chr3:73912 the reference was an A. On the forward strand (read1), there
> are 7 guanine base pairs that aligned to the reference sequence at this
> position. Additionally, on the reverse strand (read2), there are 6 guanine
> base pairs that aligned to the reference sequence at this position ( or is it
> 6 cytosine base pairs, given that it is the reverse?). This is where I am
> confused.
It may be clearer if you mock up a small SAM file and mpileup it yourself so
you can see what is going on. For example,
@SQ SN:chr3 LN:1000000
foo 0 chr3 73910 20 6M * 0 0 GGGGGG
AAAAAA
bar 16 chr3 73912 20 6M * 0 0 GGGGGG
BBBBBB
"samtools mpileup foobar.sam" gives 2 Gg AB mpileup columns at positions
73912-73915. The lowercase "g"s correspond to the bases of bar -- as viewed on
the reference sequence's forward strand, as one always does for mapped data in
SAM files, as Tom noted. This read has been reverse-complemented (flags=16), so
it was CCCCCC as viewed when it came off the sequencing machine, and it has
been mapped to the reverse strand of the reference.
> Also, what if my reference base is lowercase:
> chr3 73912 a 21 g,,..G,.gGGGgGGg,.Ggg JJ<JJJ<sJJssJJsss7JkJ
>
> Does this mean that the reference base is actually a thymine, given that it
> is from the reference genome?
No, it's an A. All that mpileup documentation about upper/lower-case and
dots/commas indicating strands pertains only to the "g,,..G,.gGGGgGGg,.Ggg"
column.
The reference base in column 3 is simply copied from your -f genome.fa file. So
your genome.fa reference genome must have a mixture of upper- and lowercase
reference bases in it. Presumably this is some kind of masking, but what it's
supposed to indicate would be a question for whoever made that reference genome
.fa file -- mpileup is not altering it in any way.
John
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