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  • pi101
    Junior Member
    • Apr 2011
    • 5

    understanding pileup indels

    Hello

    I have read the pileup docs about indels but i did not find it very clear.
    I have read this page


    Please could you tell me what this reference and genotype means

    Code:
    T      -ACTC/*
    It seems to be saying that 2 alleles were observed, one the same as the reference (*) and one a deletion of ACTC and that the reference
    became a T?????

    I believe the case where 2 alleles were found, one the same as the reference and one a deletion of ACTC relative to the reference, would have been written as


    Code:
    *      -ACTC/*
    thanks

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