Table 2.
Comparison of variant changes for each line
| Type | Total | Homozygous | Heterozygous |
|---|---|---|---|
| Fayoumi vs. RJFb | |||
| SNV | 4,146,394 | 3,638,803 | 507,591 |
| INSc | 180,752 | 158,256 | 22,496 |
| DELd | 135,321 | 125,514 | 9,807 |
| TOTAL | 4,462,467 | 3,922,573 | 539,894 |
| Leghorn vs. RJF | |||
| SNV | 4,271,399 | 4,010,609 | 260,790 |
| INS | 189,494 | 177,474 | 12,020 |
| DEL | 144,839 | 142,181 | 2,658 |
| TOTAL | 4,605,732 | 4,330,264 | 275,468 |
| Fayoumi vs. Leghorn: referencea | |||
| SNV | 3,792,327 | 3,094,177 | 698,150 |
| TOTAL | 3,792,327 | 3,094,177 | 698,150 |
Fayoumi and Leghorn vs. RJF and Fayoumi vs. the Leghornized reference genome. aFayoumi vs. the Leghornized reference genome analysis done on SNVs only
b RJF Red Jungle Fowl, c INS insertion variants, d DEL deletion variants