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Fig. 7 | Genome Biology

Fig. 7

From: The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Fig. 7

Minor allele frequency distributions and LD decay for biallelic, non-missing SNPs in the 1000 Genomes Phase 3 variant calls (N = 2504) (1KG), and the MIKK panel Illumina-based calls excluding one of each pair of sibling lines (N = 63), across all autosomes (1KG: chrs 1-22; MIKK: chrs 1-24). A Density of allele frequencies in the 1KG and MIKK panel calls. B LD decay for each autosome, calculated by taking the mean r2 of pairs of SNPs with MAF > 0.1 within non-overlapping 100-bp windows of distance from one another, up to a maximum of 10 kb. Inset: mean r2 within 100-bp windows, up to a maximum of 1 kb. LD decays faster on chromosome 2 for the MIKK panel due to its higher recombination rate, consistent with the genetic linkage map described in [58]

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