Table 2.
Genotyping summary statistics and analysis results for both the full and rarefied data sets, including the number of polymorphic sites and polymorphism rate, and HOBS based on all sites (polymorphic or monomorphic).
| Dataset | Pop | Samples/locus | Poly. sites | Poly. rate (%) | H OBS | N e (95% C.I.) | Filtered loci | Private alleles |
|---|---|---|---|---|---|---|---|---|
| Full | BC | 35.9 | 12,286 | 1.07 | 0.00278 | 9.3–9.3 | 3,722 | 58 |
| JPN | 74.7 | 19,411 | 1.70 | 0.00266 | 25,048–56,291 | 5,423 | 1,401 | |
| VIU | 63.7 | 15,471 | 1.35 | 0.00276 | 26.4–26.4 | 4,531 | 270 | |
| Rarefied | BC | 34.2 | 12,685 | 0.73 | 0.00186 | 9.5–9.5 | — | — |
| JPN | 35.7 | 17,490 | 1.00 | 0.00177 | ∞ | — | — | |
| VIU | 35.4 | 14,765 | 0.85 | 0.00184 | 22.9–23.0 | — | — |
Both data sets allow multiple variants per RAD-tag; the full data set has 21,048 variants in 1,143,426 sites, and the rarefied had 20,269 variants in 1,746,980 genomic sites. Ne was calculated based on microhaplotypes (9,377 loci). The number of filtered loci shows the number of polymorphic loci per population in single-SNP per locus data after filters in each population including per population MAF and HW (P < 0.01).