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.