Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering

Table 1

Simulated restriction-based genome sampling for the three species.

Species	Total fragments	200–800 bp fragments	Total 100 bp reads	Homozygous Tags percentage	Heterozygous Tags percentage	Mean allele divergence
Stickleback	345,704	90,974 (26.32%)	181,948	72%	28%	0.5%
Soybean	269,756	36,940 (13.69%)	73,880	39%	61%	1.5%
Ciona	61,102	7,746 (12.68%)	15,492	18%	82%	2.7%