Additional file 3.

Additional analyses carried out to test the effects of SNP calling parameters, verify called SNPs and to simulate the four-haplotypes test. Additional analyses carried out to test the effects of varying the SNP calling parameters on the numbers of SNPs called in the Rahman strain, verify the called SNPs in Rahman strain by comparison with an independently generated dataset and to simulate the four-haplotypes test under models of varying recombination and gene conversion.

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Weedall et al. Genome Biology 2012 13:R38   doi:10.1186/gb-2012-13-5-r38