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  • samtools mpileup format question

    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!

  • #2
    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.

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