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Table 1 Samples and sequencing coverage

From: Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing

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
  1. 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