Table 1.
Sources of fish, sequence data types used in the design and testing of the Arctic charr genotyping array.
Table 2.
Summary of the number of candidate SNPs derived from each data source and the number of SNPs from each data source that were included in the final array design.
Table 3.
The number of polymorphic and monomorphic SNPs observed within the different test groups of Arctic charr.
The number of polymorphisms unique to each strain (Unique to strain) and the number shared with at least one other strain (Multiple strains) are shown. ‘Total recommended’ indicates markers classified as ‘recommended’ by the Axiom Analysis Suite’s best practices workflow. Polymorphic markers include the Axiom Analysis Suite, ‘polymorphic high resolution’ and ‘no minor homozygote’. Across the four groups, 79,692 unique SNPs were recommended for use.
Fig 1.
A Venn diagram depicting the number of unique and shared polymorphic SNPs across the four groups of Arctic charr in the test set.
In total, 63,060 of the 86,503 SNPs on the Salp87k genotyping were identified as polymorphic while 21,785 were polymorphic within only one of the groups.
Table 4.
Summary table of Arctic charr reference genome coverage (GCA_002910315.2) by markers included on the 87k Arctic charr SNP genotyping array.
Fig 2.
Visual representation of the distribution of the array markers among the 39 chromosomes of the Arctic charr genome (GCA_002910315.2).
The black bars in the background represent the chromosome sequence, and each dot represents the location of SNP on the Arctic charr genotyping array. A total of 58,495 SNPs from the array are located along the chromosomes, while 26,425 additional SNPs are found on the unplaced contigs.
Fig 3.
The distribution of polymorphic markers across the Arctic charr genome identified in four test groups.
A: Fraser strain, Panel B: Nauyuk strain, Panel C: Tree River strain, Panel D: Icelandic.