Table 1 Sequence variation in four medaka inbred strains and the Kiyosu wild population from Southern Japan compared with the reference HdrR strain
StrainSNPs(as %)Genes With at Least One VariantNumber of Missense SNPsNumber of Nonsense SNPs
Nilan9,078,0501.3%16,38686,545679
HSOK9,583,4411.37%16,59083,261755
Kaga9,590,1141.37%16,60375,187742
HNI9,522,4791.36%16,61274,921711
Total inbreds20,522,8802.93%16,925175,8561,682
Kiyosu population4,797,9620.69%15,72746,639611
  • 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.