Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal

Table 1 Summary information for the seven de novo assembled sets of RAD loci

m	M	n	Number of RAD loci	Number of RAD loci present in at least 2 individuals	Heterozygosity	Average depth of coverage
2	2	1	674,500	267,069	0.09	9.46
3	1	1	423,664	227,999	0.08	10.12
3	2	0	497,830	278,376	0.13	10.55
3	2	1	378,310	208,702	0.09	10.55
3	2	2	349,082	193,859	0.08	10.55
3	3	1	343,062	198,718	0.09	10.75
4	2	1	276,717	186,925	0.09	11.48

The Stacks parameters -m and -M define the minimum number of raw reads and the maximum number of mismatches between raw reads when creating a stack within the same individual respectively. -n corresponds to the number of mismatches allowed between stacks when processing multiple individuals to construct RAD loci. For each tested combination of parameters, we report the total number of RAD loci, the number of RAD loci present in at least two individuals, observed heterozygosity (outputted by the population module within the Stacks pipeline) and average depth of coverage

ISSN: 1471-2164