6_PrepareFasta_X

Phased Haplotypes - that is, SNP and genomic location - used to produce the Dsim Recombination Map, for the X chromosome. We crossed focal males from 189 isofemale lines, from Florida, to virgin “reference” females, and then individually sequenced the F1 progeny. From the raw BAM files, we produced phased haplotype files, in which reference alleles are removed and SNPs called. This was done in FreeBayes: segment size 1kb, alpha 0.05, theta 0.04. Full details are provided in our paper. Here, we provide 189 phased haplotypes for the X chromosome. This is essentially information about SNPs and their genomic positions.