Table 1. Summary of GBS libraries.

Library	Barcodes	F2s	Adapters	Total Reads	Barcoded F2 Reads	Barcoded Reads/F2	Mapped Reads/F2	Mapped Read COV	SNP Coverage	Marker Coverage	Genotype Fail %
1a	48	12	Elshire	216	58.8	4.9	3.1	0.5	3.1	371.7	0.04
2a	48	48	Elshire	212.4	168.3	3.5	2.4	1.03	2.4	288.2	0.5
3	48	48	Elshire	418.6	397.7	8.3	5.6	1.18	0.7	85.1	5.4
4	96	96	Y-shaped	559.7	487.6	5.1	3.9	0.61	3.5	424.7	0.3
5	96	96	Y-shaped	428.2	363.1	3.8	3	0.59	2.8	228.5	1.1
6	96	96	Y-shaped	440.5	371.9	3.9	3	0.61	2.8	230.5	0.9
7b,c	384	332	Y-shaped	498	259.1	0.8	0.6	0.81	0.5	49.1	2.6
All	816	719	*	2773.3	2101.1	2.9	2.2	1.26	1.7	168.6	1.9

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).

^aFor libraries 1 and 2, the R2 read failed, resulting in half the expected number of reads.

^bApeKI digestion and adapter ligation reactions were performed at half volume to conserve costs.

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