Table 1 Description of the breeds analyzed, shared and breed-exclusive SNPs
Breed | Country | Number of samples | Wattersons variability | % missing | Mean depth | CHCU-exclusive SNPs | Shared SNPs with CHCU | Shared SNPs with CHFR | Shared SNPs with CHCA | Shared SNPs with LIMS | Shared SNPs with TXL | Shared SNPs with BRG |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
CHCU | CU | 12 | 0.0021 | 0.03 | 12.5 | 1,176,249 | – | |||||
CHFR | FR | 15 | 0.0015 | 0.06 | 11.4 | 582,972 | 10,110,342 | – | ||||
CHCA | CA | 15 | 0.0018 | 0.13 | 10.4 | 737,160 | 10,667,212 | 10,847,599 | – | |||
LIMS | FR/CA | 11 | 0.0016 | 0.21 | 8.7 | 695,594 | 9,429,688 | 9,796,472 | 9,961,440 | – | ||
TXL | US | 4 | 0.0023 | 0.08 | 10.3 | 576,849 | 8,243,412 | 7,639,145 | 8,085,077 | 7,370,881 | – | |
BRG | US | 5 | 0.0028 | 0.05 | 11.5 | 842,771 | 9,514,147 | 6,854,966 | 9,033,938 | 7,934,515 | 7,655,123 | – |
BRM | US/AU | 10 | 0.0035 | 0.11 | 10.8 | 14,929,949 | 11,442,083 | 8,653,635 | 10,134,007 | 8,267,282 | 9,169,187 | 12,519,875 |