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  • Expected insertion: deletion ratio for exome data?

    Hi Everyone,

    I am wondering what the expected insertion: deletion ratio is for your exomes? Right now I'm getting ~0.9 meaning deletions are a bit more common than insertions in the exome? Is there a reason for this?

    Thanks,

    MC

  • #2
    It common to see a deletion bias with the reference. Insertions are harder to map.

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    • #3
      Thanks for the reply. So biologically there is no reason for there to be more deletions than insertions and so this ratio should approach 1. This is probably a naiive question but why are insertions more difficult to map then deletions?

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      • #4
        Originally posted by chongm View Post
        Thanks for the reply. So biologically there is no reason for there to be more deletions than insertions and so this ratio should approach 1. This is probably a naiive question but why are insertions more difficult to map then deletions?
        No its a good question. If you have a read of fixed length and it spans an insertion then you have less sequence that can be used to map the read to the reference.

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        • #5
          Originally posted by adaptivegenome View Post
          No its a good question. If you have a read of fixed length and it spans an insertion then you have less sequence that can be used to map the read to the reference.
          I see, whereas in the case of a deletion all bases will map to the read reference.

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          • #6
            Originally posted by chongm View Post
            I see, whereas in the case of a deletion all bases will map to the read reference.
            Yes, and of course there are other factors that affect indel recall as well (like gap penalty and extension penalty, etc.)...

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