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how to determine a snp ?

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  • how to determine a snp ?

    hi, i resequenced a mutated bacteria genome, and want to detect the mutation information. at a position, i found half of the reads mapped are different from the reference, and half are the same . so some software reported it as snp, and some not. how to determine it as a SNP. how did this happened.
    thanks.

  • #2
    It could be a heterozygous SNP. Also errors can/will always occur (in sequencing, mapping), you might want to look at quality values as well.

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    • #3
      Hi,

      if you encounter an interesting SNP in your analysis, the quickest way to determine if it's real or not would be to confirm it with an independant method like PCR + Sanger ...
      Nicolas Tremblay
      Graduate Student

      Cardiovascular Genetics - Andelfinger Lab
      CHU Ste-Justine Research Center

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      • #4
        If you have a very small number of SNPs, validate them by eye. Display the alignments at the SNP position and see if the call makes sense. Ultimately of course validate via sanger.
        -drd

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        • #5
          thanks

          Originally posted by drio View Post
          If you have a very small number of SNPs, validate them by eye. Display the alignments at the SNP position and see if the call makes sense. Ultimately of course validate via sanger.
          yes, i did it by eye through Tablet. i found some reads aligned are A and some aligned are G. if all these reads are unique, how should i determinate? thaks

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          • #6
            Post here a screenshot of the alignments (tablet) for one of the snps and then we can discuss. The original SAM alignments for the SNP would help also.
            -drd

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