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Regarding Solexa data

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  • Regarding Solexa data

    What exactly does the following mean:

    63_k/nohup.out

    Output 285695310 out of 495475004 (57.7)% reads in gaps
    352330547 out of 495475004 (71.1)% reads mapped to contigs

    Regards,
    Ganga Jeena

  • #2
    Gaps refer to the stretches of unidentified nucleotides between contigs in your scaffolds.

    Perhaps the obvious is implied -- you have reads that align in gaps.

    I presume that this means that these reads don't align on contigs and therefore it is presumed that they belong in the gaps.

    Could be contamination too !

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