Table 4. Consistency of codominant genotyping on replicate 2b-RAD libraries prepared from two parents and ten progeny.

	Genotyped from Replicate 2
Genotyped from Replicate 1	Homozygous (Parent)	Heterozygous (Parent)	Homozygous (Progeny)	Heterozygous (Progeny)
Same genotype	1,527	1,578	6,813	5,307
Different, homozygous	0	8	0	401
Different, heterozygous	5	4	150	13
Agreement (%)	99.7%	99.2%	98.1%	92.8%

Note, average sequencing depths for two parents were 181× and 185× in rep1 and 190× and 235× in rep2, while for progeny, they were 37–46× in rep1 and 22–30× in rep2.