Table 1 Samples and sequencing coverage
Species | Sample | Abbreviation | HMM function | Raw coverage | Effective coverage | aCGH data | Dataset | Diversity analysis |
|---|---|---|---|---|---|---|---|---|
Dog | Chinese indigenous dog | DogCI2 | Training | 9.83 | – | No | Wang et al. | No |
Dog | Dingo | din | Analysis | 7.09 | 5.1 | No | Freedman et al. | Yes |
Dog | Basenji | mba | Analysis | 11.8 | 8.49 | Yes | Freedman et al. | Yes |
Dog | Kerry Blue Terrier | ali | Analysis | 21.28 | 15.32 | No | Fan et al. | Yes |
Dog | Boxer | bxr | Analysis | 31.27 | 22.29 | No | Fan et al. | Yes |
Dog | English cocker | cec | Analysis | 11.81 | 8.5 | No | Fan et al. | Yes |
Dog | Labrador retriever | dlr | Analysis | 12.6 | 9.07 | No | Fan et al. | Yes |
Dog | Chinese crest | jcc | Analysis | 19.04 | 13.71 | No | Fan et al. | Yes |
Dog | Standard poodle | osp | Analysis | 12.91 | 9.29 | No | Fan et al. | Yes |
Dog | Belgium Malanois | DogBM | Analysis | 10.11 | 7.57 | No | Wang et al. | Yes |
Dog | German shepherd | DogGS | Analysis | 9.56 | 5.61 | No | Wang et al. | Yes |
Dog | Tibetan Mastiff | DogTM | Analysis | 10.37 | 5.8 | No | Wang et al. | Yes |
Gray wolf | Wolf Russia | GW3 | Training | 11.1 | – | No | Wang et al. | No |
Gray wolf | Wolf China | chw | Analysis | 17.94 | 12.91 | Yes | Freedman et al. | Yes |
Gray wolf | Wolf Croatia | crw | Analysis | 9.73 | 6.94 | No | Freedman et al. | Yes |
Gray wolf | Israeli wolf | isw | Analysis | 7.37 | 5.26 | No | Freedman et al. | Yes |
Gray wolf | Wolf Great Lakes | glw | Analysis | 26.8 | 19.3 | Yes | Fan et al. | Yes |
Gray wolf | Wolf India | inw | Analysis | 27.42 | 19.74 | Yes | Fan et al. | Yes |
Gray wolf | Wolf Iran | irw | Analysis | 30.15 | 21.71 | Yes | Fan et al. | Yes |
Gray wolf | Wolf Italy | ita | Analysis | 7.59 | 6.07 | Yes | Fan et al. | Yes |
Gray wolf | Wolf Mexico | mxa | Analysis | 25.64 | 18.46 | Yes | Fan et al. | Yes |
Gray wolf | Wolf Mexico | mxb | Analysis | 7.08 | 5.66 | No | Fan et al. | No |
Gray wolf | Wolf Portugal | ptw | Analysis | 28.46 | 20.49 | Yes | Fan et al. | Yes |
Gray wolf | Wolf Spain | spw | Analysis | 28.88 | 20.79 | Yes | Fan et al. | Yes |
Gray wolf | Wolf Yellowstone | ysa | Analysis | 28.21 | 20.31 | Yes | Fan et al. | Yes |
Gray wolf | Wolf Yellowstone | ysb | Analysis | 18.82 | 13.55 | Yes | Fan et al. | No |
Gray wolf | Wolf Yellowstone | ysc | Analysis | 8.44 | 6.75 | Yes | Fan et al. | No |
Gray wolf | Wolf China | GW4 | Analysis | 9.61 | 6.75 | No | Wang et al. | No |
Coyote | Coyote California | cac | Training | 26.87 | 19.35 | No | Fan et al. | No |
Coyote | Coyote Alabama | alc | Analysis | 7.69 | 5.54 | No | Fan et al. | No |
Coyote | Coyote Midwest | mwc | Analysis | 9.11 | 6.56 | No | Fan et al. | No |
Jackal | Golden Jackal Kenya | jaa | Analysis | 27.47 | 19.78 | Yes | Freedman et al. | No |
Red wolf | Red wolf | rwa | Analysis | 30.28 | 21.8 | No | Fan et al. | No |
Red wolf | Red wolf | rwb | Analysis | 7.72 | 6.17 | No | Fan et al. | No |