Table 3.

Main statistics of ddRAD libraries, mapping and SNP detection.

	n	Total reads family	Av. raw reads	Av. reads stacks	PA (%)	Unmapped	loci	mean cov	n_gts
F1	76	244,900,564	6,444,752	6,215,911	88.23	0.34%	23,828	146	22,040
F2	95	398,313,256	8,385,542	8,090,267	89.71	0.33%	24,978	190	22,823
F3	67	226,072,540	6,649,192	6,090,258	86.20	0.32%	26,068	132	24,054
F4	79	248,271,546	6,130,162	5,972,512	87.74	0.33%	25,525	135	23,157
F5	48	280,609,738	11,692,072	11,384,985	88.13	0.33%	30,005	237	27,011
F6	65	363,499,961	11,184,614	10,899,007	88.04	0.31%	27,742	242	24,883
F7	62	337,573,225	10,889,459	10,627,007	88.93	0.34%	30,550	226	26,773
F8	73	447,768,745	12,267,637	11,674,383	89.42	0.33%	28,002	260	25,371
Parents	8	39,815,609	8,847,913	8,323,338	86.08	0.36%	17,632	242	15,898

The total number of individuals analysed (n), the total reads per family, the average number of paired-end reads per individual, the average number reads used by stacks, the % of primary alignment and unmapped reads, number of loci, effective coverage, and number of genotypes (n_gts).