Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness

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.

Information^1	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

Qm = mapping quality; RD = read depth; Rdup = removed duplicates.