Table 1.
Frequency of SNPs in different comparisons of RJF and the 3 domestic chicken lines. In addition, we show comparisons involving 3.8-Mb of finished BAC sequence from another line of the layer (White Leghorn) breed. SNP rates are an estimate of nucleotide diversity (π), as embodied by the effective length, which considers how much of the data is of sufficiently good quality to actually detect SNPs and the probability that overlapping reads might be derived from homologous chromosomes
| # of SNPs | L(effective) | SNP/kb | |
|---|---|---|---|
| Wild versus domestic | |||
| RJF-Broiler | 1,041,948 | 197,431,517 | 5.28 |
| RJF-Layer | 889,377 | 170,586,544 | 5.21 |
| RJF-Silkie | 1,217,817 | 217,841,171 | 5.59 |
| Between domestic lines | |||
| Broiler-Layer | 194,605 | 37,506,800 | 5.19 |
| Broiler-Silkie | 257,849 | 47,554,311 | 5.42 |
| Layer-Silkie | 246,954 | 42,682,304 | 5.79 |
| Within domestic lines | |||
| Broiler-Broiler | 59,227 | 13,835,075 | 4.28 |
| Layer-Layer | 40,412 | 10,863,595 | 3.72 |
| Silkie-Silkie | 83,630 | 15,253,383 | 5.48 |
| Compare to layer BACs | |||
| RJF-to-BAC | 20,925 | 3,809,567 | 5.49 |
| BAC-Broiler | 4,404 | 847,456 | 5.20 |
| BAC-Layer | 3,904 | 740,392 | 5.27 |
| BAC-Silkie | 5,089 | 925,738 | 5.50 |