We generated 162 million 100-bp paired-end reads. The yam transcriptome size has been estimated to be approximately 64 Mb  and the genome size to be 550 Mb. We obtained an average mapping rate of ~ 12.6% of our genomic reads i.e. close to the expected 12.4% based on the relative transcriptome size compared to the whole genome (Additional file 2: Table S2). We identified a total of 308,840 SNPs. These SNPs were found in 23,136 contigs with a mean contig length of 1316 bp (ranging from 250 to 15,691). A low correlation was observed between the length of the contigs and the number of SNPs detected (r = 0.34, p < 0.001).