From: Evaluation of variant identification methods for whole genome sequencing data in dairy cattle
Calling method | Total number of SNVs | Total number of InDels | Transition/Transversion ratio | |||
---|---|---|---|---|---|---|
Single sample calling, combined | Multi sample calling | Single sample calling, combined | Multi sample calling | Single sample calling, combined | Multi sample calling | |
HC | - | 19,901,885 | - | 2,685,032 | - | 2.138 |
PL | 17,709,672 | 16,894,054 | 2,973,025 | 2,890,066 | 2.178 | 2.165 |
PL_PRIM | 20,869,015 | 19,759,134 | 2,864,147 | 2,890,412 | 2.105 | 2.058 |
SAM | 20,647,891 | 18,767,273 | 2,682,094 | 1,997,791 | 2.176 | 2.240 |
UG | 21,984,283 | 22,048,382 | 2,485,677 | 2,741,468 | 2.024 | 1.974 |