Table 1 Arrays used in this study, numbers of variants per array, number of retained variants from the WGS data, before and after quality control (QC), whether imputation was successful or not
Array | Number of variants on the array | Number of variants retained from WGS before QC | Number of variants retained from WGS after QC | Imputation successful or not |
|---|---|---|---|---|
HD | 777,962 | 685,468 (88%) | 409,013 (53%) | Yes |
BOS1 | 648,875 | 595,938 (92%) | 257,217 (40%) | Yes |
GGPF250 | 227,234 | 137,609 (61%) | 51,803 (23%) | Yes |
GGPHDV3 | 139,977 | 125,712 (90%) | 72,456 (52%) | Yes |
GGP90KT | 76,999 | 70,603 (92%) | 40,749 (53%) | Yes |
IND90KH | 74,150 | 66,879 (90%) | 42,484 (57%) | Yes |
ZMD2 | 68,213 | 53,314 (78%) | 25,223 (37%) | Yes |
ZOETIS1 | 59,825 | 45,559 (76%) | 22,657 (38%) | Yes |
BOVMD | 57,134 | 43,860 (77%) | 20,151 (35%) | Yes |
IDBV3 | 53,450 | 44,447 (83%) | 20,711 (39%) | Yes |
SNP50V3 | 53,218 | 47,788 (90%) | 21,341 (40%) | Yes |
ANGGS | 49,541 | 44,082 (89%) | 21,957 (44%) | Yes |
BOVG50V1 | 47,844 | 41,214 (86%) | 25,304 (53%) | Yes |
GGPIND35 | 35,339 | 31,903 (90%) | 22,253 (63%) | Yes |
GGPLDV4 | 30,105 | 26,330 (87%) | 16,072 (53%) | Yes |
GGPLDV3 | 26,504 | 23,035 (87%) | 14,216 (54%) | Yes |
ZLD4 | 20,503 | 17,378 (85%) | 9358 (46%) | No |
ZLD2 | 18,206 | 15,769 (87%) | 8649 (47%) | No |
GGPLDV1 | 8762 | 6265 (71%) | 3645 (42%) | No |
BOVLDV2A | 7931 | 7163 (90%) | 4234 (53%) | No |
BOVLDC | 6909 | 6305 (91%) | 3670 (53%) | No |
DAIRYULDB | 4227 | 3651 (86%) | 2276 (54%) | No |
BOVGGPV3K | 2900 | 2603 (90%) | 1720 (59%) | No |