Table 1. Results of Arabidopsis thaliana Sanger sequencing.

Position in bubbleparse list	SNPs sequenced	Confirmed SNPs	Unconfirmed SNPs	Problems with sequencing	Number in curated list
Top	48	46	0	2	39
25%	16	15	0	1	13
50%	16	15	0	1	10
75%	16	15	0	1	11

From the ranked list of all SNPs predicted by Bubbleparse in contigs of over 200 nt, the top 48, as well as 16 from 25%, 50% and 75% down the list were tested with Sanger sequencing. This confirmed all but 5 as being real SNPs between Col-0 and Ler-1. The remaining five all had sequencing problems – such as the sequence ending before the SNP was reached – so are not confirmed as false postives.