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 |
Sequences were retrieved from previously published work from Fan et al. [57], Freedman et al. [4] and Wang et al. [56]. The raw coverage is calculated from the total number of reads before mapping and referred to the 2,413,045,422 bps of the prepared version of CanFam3.1. The effective coverage is calculated after removing poor-quality sequencing lanes and read ends. For 14 samples aCGH data from Ramirez et al. [43] were available. Coyote, jackal and red wolf samples were combined as a single group for the analyses