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
"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
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