Bovine genomes used during successive TrioTrain iterations
| Training: Parents | Evaluation: Offspring | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Trio name | SRA accession | Sex | Breed code | Mean cov. | SRA accession | Sex | Breed code | Mean cov. | |
| Training phase 1 | |||||||||
| 1 | Trio1 | SAMN10940502 | M | AA | 35.96 | SAMN10940538 | F | AA | 23.64 |
| 2 | SAMN10940537 | F | AA | 23.10 | |||||
| 3 | Trio2 | SAMN10598569 | M | HE | 17.47 | SAMN10598563 | F | HE | 14.45 |
| 4 | SAMN10598566 | F | HE | 12.92 | |||||
| 5 | Trio3 | SAMEA4644756 | M | BS | 15.84 | SAMEA4644754 | F | BS | 16.78 |
| 6 | SAMEA4644755 | F | BS | 15.14 | |||||
| 7 | Trio4 | SAMN15780082 | M | HO | 35.23 | SAMN15779741 | M | HO | 23.66 |
| 8 | SAMN15779919 | F | HO | 46.68 | |||||
| 9 | Trio5 | SAMN10598570 | M | HE | 13.51 | SAMN10598562 | F | HE | 15.89 |
| 10 | SAMN10598567 | F | HE | 15.08 | |||||
| 11 | Trio6 | SAMEA5159887 | M | TG | 21.63 | SAMEA5159888 | F | TG | 20.41 |
| 12 | SAMEA5159889 | F | TG | 19.77 | |||||
| Training phase 2 | |||||||||
| 13 | Trio7 | SAMN15779644 | M | HJ | 39.35 | SAMN15779593 | F | HJ | 50.83 |
| 14 | SAMN15779569 | F | HJ | 44.75 | |||||
| 15 | Trio8 | SAMN15779606 | M | HJ | 30.81 | SAMN15779717 | M | HJ | 27.65 |
| 16 | SAMN15779596 | F | HJ | 39.31 | |||||
| 17 | Trio9 | SAMN10598569 | M | HE | 17.47 | SAMN10598564 | M | HE | 14.79 |
| 18 | SAMN10598565 | F | HE | 14.62 | |||||
| Training phase 3 | |||||||||
| 19 | Trio10 | SAMN05788493 | M | BI | 22.69 | SAMN13655887 | F | BI | 17.95 |
| 20 | SAMN13655886 | F | BI | 23.72 | |||||
| 21 | Trio11 | SAMN05788493 | M | BI | 22.69 | SAMN10940703 | M | BI | 24.06 |
| 22 | SAMN10940702 | F | BI | 23.78 | |||||
| Training phase 4 | |||||||||
| 23 | Trio12 | SAMN08473804 | M | AA | 36.99 | SAMN08473802 | M | F1X | 50.01 |
| 24 | SAMN08473803 | F | BR | 43.32 | |||||
| 25 | Trio13 | SAMN12153485 | M | HI | 34.69 | SAMN12153487 | F | F1X | 17.92 |
| 26 | SAMN12153486 | F | YK | 10.66 | |||||
| 27 | Trio14 | SAMN16823422 | M | BI | 27.44 | SAMN16780309 | M | F1X | 14.46 |
| 28 | SAMN16825967 | F | SI | 35.42 | |||||
| Training phase 5 | |||||||||
| 29 | Trio15 | SAMN08473804 | M | BI | 36.99 | SYNTHETIC | M | F1X | 26.20 |
| 30 | SAMN08473803 | F | SI | 43.32 | |||||
[i] Individual genomes have a distinct “truth” VCF. Extending DeepVariant with bovine genomes was achieved over five phases with 30 TrioTrain iterations, representing 14 family trios and one synthetic hybrid offspring. Additional details are provided in Supplemental Table S4. Breed code abbreviations are as follows: (AA) Angus, (HE) Hereford, (BS) Brown Swiss, (HO) Holstein, (TG) Tyrolean Grey, (HJ) Holstein–Jersey, (BI) bison, (BR) Brahman, (HI) Scottish Highlander, (YK) yak, (SI) Simmental, and (F1X) F1 hybrid cross.