Table 1 Summary and annotation of SNPs in Duroc pigs
CategoryWGSGBS
Sample size27423282
Average depth (X)12.1012.7911.9816.921
Average genome coverage (%)96.5699.0396.130.56
Average Mapping rate (%)99.6799.6699.6795.95
High-quality base (Gb)817.35127.98689.3745.49
Q20 (%)97.3695.2397.7398.13
Q30 (%)91.1889.6791.4491.91
Number of total SNP14,827,5499,245,51113,787,663651,425
Upstream92,78556,48785,6344,094
UTR528,43618,07026,1011,917
ExonicStopgain545265504215
Stoploss1176511427
Synonymous66,28541,37961,3675,663
Nonsynonymous44,66026,35241,24310,212
Unknown15233144215
Splicing614397565254
Intronic5,496,3753,459,3595,108,598192
UTR3133,19482,605124,775281,638
UTR5/UTR37024546798,489
Downstream98,20759,70091,14553
Upstream/downstream2,3281,4552,1644,852
Intergenic8,863,1495,498,8908,244,630144
  • 1 the population sequencing depth.