Table 1.
Variants discovered by breed type
| Fayoumi | Leghorn | aFayoumi vs. Leghornized reference | |
|---|---|---|---|
| Depth of coverage | ~24× | ~22× | ~24× |
| Assembly coverage | 84.5 | 93.7 | 84.5 |
| Total variants | 4,462,467 | 4,605,732 | 3,792,327 |
| Previously uncharacterized variants | 3,223,583 | 3,287,720 | 3,791,430 |
| Homozygosity | 99.9482 % | 99.9736 % | 99.9330 % |
| bTs/Tv (All Variants) | 2.371 | 2.365 | 2.286 |
| Change rate | 1 change every 235 bases | 1 change every 227 bases | 1 change every 276 bases |
Total reads computed using GATK DepthofCoverage. Assembly coverage and Sequence coverage calculated using Samtools and GATK DepthofCoverage. All other data calculated using SnpEff. All data is pre-filter. aFayoumi vs. Leghorn only compared using SNV data; indels were excluded along with Chromosomes Z and W. bTs/Tv is the ratio of transitions/transversions within each population