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  • Bueller_007
    started a topic Odd characters in samtools mpileup output

    Odd characters in samtools mpileup output

    I'm struggling to figure out what some of the characters in my samtools mpileup output are. Here's one of the offending bases (scaffold1:25513). There are many.

    Code:
    scaffold1       25513   G       20      <<,,,,,a,A,aa,a,AA..    #A.CCFG6G6F67E:F<6GF
    So it tells me that the read depth is 20, and this is confirmed by counting the number of characters in each of the last two columns. But I have absolutely no idea what the "<" character represents in the read_bases column (column #5).

    The only special characters I'm expecting to see are '.' and ',' (indicating forward and reverse matches) '+' and '-' (indicating indels), and '^' (followed by a symbol indicating read-mapping quality) and '$' (indicating the beginning and end of a read respectively).

    So can anyone tell me what '<' means in column 5?


    EDIT: To answer my own question somewhat, '<' and '>' indicate a "reference skip" according to the mpileup documentation. (Although they are not mentioned in the pileup format documentation, which is why I couldn't find them.) However, I have absolutely no idea what "reference skip" means, so I'm still out of luck. If it's referring to a base that is not covered (e.g. due to splicing) then shouldn't the coverage ideally be reported as 18, not 20?
    Last edited by Bueller_007; 08-26-2011, 04:52 PM.

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