Table 5. Concordance between genotyping-by-sequencing and KASP genotyping calls.

	Expected genotype call (KASP)
Genotyping-by-sequencing	Nulliplex	Simplex	Duplex	Triplex	Quadruplex	Total
Concordant calls	4,975	4,861	2,204	1,373	1,272	14,685
Discordant calls	67	25	86	34	25	237
Percentage of concordant calls	98.7%	99.5%	96.2%	97.6%	98.1%	98.4%
Median read-depth of concordant calls	85×	91×	101×	92×	75×	89×
Median read-depth of discordant calls	52×	56×	73×	83×	47×	61×
Percentage of alternative reads for concordant calls	0%	23%	49%	76%	100%	–
Percentage of alternative reads for discordant calls	4%	36%	34%	56%	97%	–

The genotype calls derived from each method for 270 binary SNPs were compared. Sequencing calls were filtered by a minimum read depth of 15× and a minimum genotype quality score of GQ26.