samtools mpileup format question

[lre1234]

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!

[swbarnes2]

Copied and pasted from the samtools sourceforge page:

"Also at the read base column, a symbol `^' marks the start of a read segment which is a contiguous subsequence on the read separated by `N/S/H' CIGAR operations. The ASCII of the character following `^' minus 33 gives the mapping quality. A symbol `$' marks the end of a read segment."

The last column is the base qualities. It's your data, so you should know or be able to find out how its scaled. There is a '?' and ']' which don't make a lot of sense together. You should understand fastq format, that's where the quality scores came from.