Table 1  Characteristics of linked intervals identified by whole-genome sequencing
Zebrafish mutantamotowddhlwfrntsump
Whole-genome sequencing
 No. reads (106)6181607983
 Genome coverage2.6×2.7×2.8×3.9×4.1×
Size of the linked intervalb
 Region of reduced heterogeneityc
  Physical size (Mb)354264619
  Genetic size (cM)<25<30<25<18<18
 Region of homogeneityd
  Physical size (Mb)194558
  Genetic size (cM)<14<30<4<3<11
Coding sequence coverage in linked intervale
 ≥1 read93%92%87%95%88%
 ≥2 reads83%77%76%92%85%
Homogeneous SNPs in linked intervalf
 Total7640225107177839518
 Not in dbSNPg5984223102364319110
 Noncoding566320799763038687
 Synonymous229121789287
 Nonsynonymous924939136
 Uniqueh
  Noncoding38122179106
  Synonymous00002
  Nonsynonymous2 (63)i1 (119)0 (22)0 (4)0 (7)
  • a minamoto (motot31533), welded (wddt31169), hollow (hlwt3373), fruehrentner (frntt31786), and schrumpfkopf (sumpt3625).

  • b Intervals identified by a high mapping score; linkage was confirmed by analysis of SSLP or SNP markers.

  • c Region with a reduction in heterogeneity of at least 30% compared to the genome-wide average.

  • d Defined as a region with a >90% reduction in heterogeneity compared to the genome-wide average.

  • e Coding sequence of RefSeq and Ensembl genes.

  • f Detected homogeneous variants covered by at least two sequencing reads.

  • g Homogeneous variants not present in the publicly available SNP database (dbSNP) downloaded from Ensemble.

  • h Homogeneous variants not present in the reference strain database established in this study.

  • i The number of unique nonsynonymous mutations covered by only one sequencing read.