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  • SNP enrichment test along the genome

    Hello, there,

    I have SNP annotation along the genomic DNA. By visual inspection, I can tell that some chromosomal region tends to have more SNPs than the other. I wonder if there is a tool to statistically analysis such enrichment along the genome?

    For example, I can calculate the number of SNPs along each 5k genome region, and also the average number of SNPs long the whole genome (total number/length of genome), how would I find the genomic regions that have significant higher number of SNPs when compared with this average SNP number?

    Thanks a lot!

    C.

  • #2
    fisher exact test maybe fit this.

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