Table 1. Sequence variation in four medaka inbred strains and the Kiyosu wild population from Southern Japan compared with the reference HdrR strain.

Strain	SNPs	(as %)	Genes With at Least One Variant	Number of Missense SNPs	Number of Nonsense SNPs
Nilan	9,078,050	1.3%	16,386	86,545	679
HSOK	9,583,441	1.37%	16,590	83,261	755
Kaga	9,590,114	1.37%	16,603	75,187	742
HNI	9,522,479	1.36%	16,612	74,921	711
Total inbreds	20,522,880	2.93%	16,925	175,856	1,682
Kiyosu population	4,797,962	0.69%	15,727	46,639	611

Numbers are given for pairwise comparison with HdrR (the reference) and compared with the 17,442 genes on chromosome scaffolds of the 19,686 genes in the medaka reference gene annotation. The counts include both homozygous and heterozygous sites in each inbred strain (0.1% of divergent sites are heterozygous for Hsok, Kaga, and HNI; 1% for Nilan). The results for the Kiyosu population include SNPs detected in at least a single individual in either homozygote or heterozygote. See Materials and Methods for details on the SNP quality thresholds used, the sequencing coverage and the genotyping methods used for the inbred strains and the Kiyosu population. SNP, single-nucleotide polymorphism.