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. 2015 Apr 20;10(4):e0124781. doi: 10.1371/journal.pone.0124781

Fig 1. SNP development and genotyping pipeline for cotton RAD markers.

Fig 1

Raw reads were aligned to the TM-1 reference genome with BWA software. After filtering and SNP calling, the putative SNPs were divided into three types: simple SNPs with one allele per parent, and complex SNPs which with one allele from one parent and two alleles from the other parent or SNPs with two alleles from both parents.