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Mouse SNP

PERLEGEN and 454 SNP HAPLOTYPE FORM

Link to example of SNP haplotype  Viewer

Displays graphical representations of SNP and haplotypes of C57BL/6, A/J, BALB/CBYJ, 129S1/SvImJ and C3H/HeJ for any region of the mouse genome based on Perlegen SNP. Additional data for Mmu17 30637692 to 36837814 (NCBI37) is from our own resequencing. Tables of data underlying all displays can be downloaded. A more detailed description of how the data was obtained and how it can be interpreted is available for download. Haplotypes for other strain combinations in the Perlegen dataset can be calculated on request to Harry Noyes

Enter coordinates for the region of interest. If your region includes Tir1 (Chromosome 17 30637692..36837814 NCBI37) then a haplotype plot that includes our 454 sequence data will be displayed. A plot will be displayed and a link to a file that you can download. Co-ordinates are for NCBI37 Ensembl55. Comments/suggestions to Harry Noyes

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Threshold distance for assignment to haplotype block . This is the Jukes Cantor distance above which strains will be allocated to different haplotype alleles. The default of 0.00005 corresponds to two standard deviations below the mean distance. This is appropriate where high confidence is required in allocation of shared haplotypes. See the detailed description for more information