Hi all,
I am making SNP calls using samtools and have a question about the format of the mpileup file.
for example, I got this output that looks like this:
1 8022856 A 19 .$.$.$.$..........^F.^F.^F.^F.^F. T?OM]]][][\[TWHQ/L)
I understand the first four columns (chr, position, ref base, read depth). but for the fifth colum, I am not sure I understand the different characters. Here a dot would be a match to the reference base, a comma would be a match to the reference on the reverse strand. My confusion is on the other characters that are here. Does a $ indicate that a specific read ended here? What does ^F stand for?
Also, the last column is for the mapping quality? what does each individual symbol in that represent?
Thank you all for your help!
I am making SNP calls using samtools and have a question about the format of the mpileup file.
for example, I got this output that looks like this:
1 8022856 A 19 .$.$.$.$..........^F.^F.^F.^F.^F. T?OM]]][][\[TWHQ/L)
I understand the first four columns (chr, position, ref base, read depth). but for the fifth colum, I am not sure I understand the different characters. Here a dot would be a match to the reference base, a comma would be a match to the reference on the reverse strand. My confusion is on the other characters that are here. Does a $ indicate that a specific read ended here? What does ^F stand for?
Also, the last column is for the mapping quality? what does each individual symbol in that represent?
Thank you all for your help!
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