Table 1.
Summary of sequencing data obtained from the two reduced representation libraries (RRLs) of the positive (Pos_HaeIII) and negative (Neg_HaeIII) back fat thickness estimated breeding value DNA pools.
| Information1 | Pos_HaeIII | Neg_HaeIII | Pos + Neg HaeIII |
|---|---|---|---|
| Sequenced reads | 3,581,496 | 3,887,066 | 7,468,562 |
| Reads after preprocessing | 3,390,796 | 3,731,776 | 7,122,572 |
| Removed duplicates | 698,191 | 845,961 | 1,544,152 |
| Mapped reads (Qm > 20; Rdup) | 1,449,838 | 1,476,125 | 2,925,963 |
| Sequenced bases (Qm > 20; Rdup) | 137,429,598 | 145,859,611 | 256,880,473 |
| Mean and max depth of coverage (Qm > 20; Rdup) | 1.18; 209 | 1.16; 217 | 1.29; 426 |
| Sequenced bases (Qm > 20; RD ≥ 3; Rdup) | 3,394,898 | 3,057,171 | 3,942,266 |
| Sequenced bases retained by SNAPE (Qm > 20; RD ≥ 3; Rdup) | 3,369,555 | 3,034,731 | 237,969 (in common) |
| SNPs (Qm > 20; RD ≥ 3; Rdup) | 10,694 | 10,339 | 39,165 |
1Qm = mapping quality; RD = read depth; Rdup = removed duplicates.