Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication

Table 4 SNP validation comparison using a transcriptome dataset from polyploid wheat

	Original study	Window 80,	Window 80,	Window 40,	Window 10,
	Original study	SNP score > 0	SNP score > 0.25	SNP score > 0	SNP score > 0
Validated SNPs	64	40 (37)	28 (22)	35 (34)	18 (23)
False-positives	61	3 (6)	1 (0)	2 (1)	3 (8)
False-positive rate	49%	7% (14%)	3% (0%)	5% (3%)	14% (26%)

The number of SNPs from the original study and from different settings using our strategy. There are multiple numbers per parameter explored. These reflect different alignment programs used under these settings. The first set of numbers were from Novoalign alignments, and the second were from Megablast (in parentheses).

ISSN: 1471-2105