Table 1 Summary of GBS libraries
LibraryBarcodesF2sAdaptersTotal ReadsBarcoded F2 ReadsBarcoded Reads/F2Mapped Reads/F2Mapped Read COVSNP CoverageMarker CoverageGenotype Fail %
1a4812Elshire21658.84.93.10.53.1371.70.04
2a4848Elshire212.4168.33.52.41.032.4288.20.5
34848Elshire418.6397.78.35.61.180.785.15.4
49696Y-shaped559.7487.65.13.90.613.5424.70.3
59696Y-shaped428.2363.13.830.592.8228.51.1
69696Y-shaped440.5371.93.930.612.8230.50.9
7b,c384332Y-shaped498259.10.80.60.810.549.12.6
All816719*2773.32101.12.92.21.261.7168.61.9
  • For each library, the number of barcodes and F2 fish included is listed. Total reads, barcoded F2 reads, barcoded reads/F2, and mapped reads/F2 are reported in units of millions of reads. Genotype fail % indicates percentage of final genotypes that were missing. COV, coefficient of variance (mean/standard deviation).

  • a For libraries 1 and 2, the R2 read failed, resulting in half the expected number of reads.

  • b ApeKI digestion and adapter ligation reactions were performed at half volume to conserve costs.

  • c Library 7 included nine F2 samples that were sequenced in libraries 1–6 but had very low sequencing coverage.