Results of Solanum Sanger sequencing.

We chose 27 predicted SNPs to test with Sanger sequencing. These were chosen from the Bubbleparse ranked list according to four sets of criteria, with all SNPs placed within the top 22,000 of the 68,000 linked SNPs at the expected heterozygosity. The largest number, 10, were chosen from the top of the list, which contains bubbles which are close to the expected allele ratio and also of high coverage. A second group were chosen which were very close to the expected allele ratio, but not such good coverage. A third group had very good coverage, but were not so close to the expect allele ratio. Finally, a fourth group was chosen which had high quality scores, but not necessarily as close a ratio or as good a coverage as previous groups. Overall, we found a high rate of true SNPs – with 23 out of 27 sequences containing a SNP in the position predicted by Bubbleparse, of which 14 displayed the predicted heterozygous alleles. The group chosen from the top of the ranked list showed high accuracy, with 9 out of 10 SNPs confirmed, but high rates were also shown for the other groups, though sample sizes were small.