Table 2 Consistency of genotype calls between the GBS and 90 K arrays of 96 wheat accessions. The SNPs with MAF > 0.01 and missing rate < 20% were used for comparison
Chromosome | Number and missing rate of 90K_Refv2 SNPs | Number and missing rate of GBS SNPs | Number and agreement percentage of shared markers |
|---|---|---|---|
1A | 1510 (0.34%) | 473 (11.20%) | 0 |
1B | 1883 (0.27%) | 548 (11.45%) | 2 (100%) |
1D | 847 (0.26%) | 271 (10.56%) | 0 |
2A | 1585 (0.16%) | 662 (11.33%) | 0 |
2B | 2269 (0.24%) | 1023 (11.10%) | 6 (98.65%) |
2D | 882 (0.15%) | 287 (11.13%) | 1 (100%) |
3A | 1302 (0.13%) | 555 (10.95%) | 4 (92.39%) |
3B | 1659 (0.18%) | 893 (11.03%) | 5 (100%) |
3D | 504 (0.17%) | 382 (11.33%) | 0 |
4A | 1138 (0.21%) | 448 (11.50%) | 0 |
4B | 917 (0.10%) | 318 (11.52%) | 3 (100%) |
4D | 347 (0.12%) | 99 (12.14%) | 0 |
5A | 1430 (0.24%) | 572 (11.00%) | 8 (99.58%) |
5B | 1823 (0.12%) | 784 (10.89%) | 6 (99.81%) |
5D | 455 (0.07%) | 131 (11.07%) | 0 |
6A | 1461 (0.18%) | 504 (11.08%) | 5 (92.06%) |
6B | 1542 (0.38%) | 870 (11.43%) | 2 (100%) |
6D | 547 (0.28%) | 227 (11.35%) | 2 (97.59%) |
7A | 1733 (0.29%) | 873 (11.02%) | 1 (100%) |
7B | 1494 (0.24%) | 935 (11.28%) | 1 (98.81%) |
7D | 522 (0.23%) | 257 (11.24%) | 0 |
Unknown | 163 (0.51%) | 102 (10.61%) | 0 |
Overall | 26,013 (0.22%) | 11,214 (11.17%) | 46 (97.98%) |