samtools pileup format

[foxyg]

The document regarding the pileup says
"Upper case letters are mismatches on the forward strand whereas lower case letters are mismatches on the reverse strand."

I have a line of pileup file read like this without using the -c option

chrM 9 A 5 GGGgg CCC*>



This means I have 5x depth on this location 9 of chrM, the ref is A, but I read 3 big G and 2 small g. I am assuming the big G means I actually read a G instead of A. But I am not sure how to explain the small g, does it mean I read a C in the reverse strand or a G in the reverse strand?



It is very important I get this right.



Thanks

[epigen]

Your read mapped to the reverse strand, where you observe a C instead of the T from the reference genome. The reverse complement (g) is shown in the pileup because this always refers to the forward strand (reference: A).

[foxyg]

if you use -c option with pileup and use samtools.pl to generate a consensus fasta sequence file. There are many bases are in lower case in the fasta file. Do those lower cases mean repeats or something else?

[westerman]

After looking at the code, it appears that the lower-case bases are positions where there are gaps in the mapping; e.g., no reads mapped to those positions.