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YFull Novel SNPs

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  • YFull Novel SNPs

    In answer to my question, "Would you share the filter parameters used at YFull to separate Novel SNPs into Best qual, Acceptable qual and Ambiguous qual groups?
    Their response: "Not all of them:
    Best qual: 5 reads and more, 100% quality.
    Acceptable qual: 3 reads and more, 91% quality and more.
    Ambiguous qual: 2 reads and more, 85% quality and more.
    Quality means percent of right value in all reads of this position.
    And we use some heuristics for regions also."

    Now a question remains; Why is there multiple "Reads"? One of my "Best Novel SNPs" showed T for all 141 Reads (Ref = C).