White-tailed deer SNPs (VCF file)

We detected SNPs using CLC’s quality-based variant detection algorithm (min. average quality of five flanking bases on either side of SNP = 15; min. quality of central base = 20; min. coverage = 20; max. coverage = 1000; min. variant frequency = 15%; min. variant count = 4), discarding all reads with non-specific alignments. Multiallelic SNPs were discarded as they may result from incorrect alignment of reads from paralogous genes in the transcriptome data. All SNPs have been submitted to dbSNP and will be available online in the October 2013 update. This VCF file is available in the interim.