TABLE 1.
Summary of sequencing data and SNPs in DLW, DU, and EWB
| Fields | DLW | DU | EWB | Overall |
|---|---|---|---|---|
| Sample counts | 28 | 27 | 23 | 78 |
| Average depth (X) | 23.52 | 12.43 | 9.67 | 15.21 |
| Average genome coverage (%) | 99.31 | 96.56 | 86.77 | 94.21 |
| Average mapping rate (%) | 99.44 | 99.67 | 99.77 | 99.63 |
| High‐quality bases (Gb) | 1603.98 | 817.35 | 541.45 | 2,962.79 |
| Q20 (%) | 95.48 | 97.36 | 97.89 | 96.91 |
| Q30 (%) | 89.21 | 91.18 | 91.50 | 90.63 |
| SNP categories | ||||
| Number of total SNP | 10,635,485 | 7,918,935 | 8,582,578 | 10,809,276 |
| Upstream | 62,281 | 41,584 | 45,258 | 63,487 |
| UTR5 | 19,118 | 11,141 | 11,555 | 19,373 |
| Stop gain | 278 | 186 | 205 | 279 |
| Stop loss | 58 | 38 | 40 | 58 |
| Exonic | ||||
| Synonymous | 45,246 | 27,575 | 28,412 | 45,553 |
| Nonsynonymous | 24,919 | 16,006 | 16,787 | 25,200 |
| Unknown | 37 | 77 | 126 | 135 |
| Splicing | 376 | 240 | 276 | 382 |
| Intronic | 4,112,359 | 3,011,754 | 3,246,827 | 4,178,406 |
| UTR3 | 99,978 | 70,233 | 75,627 | 101,392 |
| UTR5/UTR3 | 534 | 315 | 316 | 538 |
| Downstream | 67,917 | 47,606 | 51,334 | 69,160 |
| Upstream/downstream | 1,863 | 1,168 | 1,242 | 1,885 |
| Intergenic | 6,200,521 | 4,691,012 | 5,104,573 | 6,303,428 |
Abbreviations: DLW, Danish large white; DU, Duroc; EWB, European wild boar.