This track shows the single nucleotide polymorphisms (SNPs) and/or insertions/deletions (indels) determined by the Beijing Genomics Institute (BGI). Genomic sequence reads from 3 alternate strains of chicken (Broiler, Layer and Silkie) were used to determine the SNPs relative to the reference assembly for Red Jungle Fowl (RJF). SNPs and indels are associated with genes (annotations by BGI until Ensembl annotations are ready). Information on the association can be displayed along with a link to the details page for the gene.
SNP names are of the format snp.[supercontig].[contig].[position].[type].[strain]:
Sequence reads from the Broiler, Layer and Silkie strains were mapped to the reference chicken assembly with blast. Then, cross_match was used for the detailed base-by-base comparison. The Phred quality scores (-10 * log 10 estimated error probability) are given for the SNP base(s) in the assembly and the (single read) SNP read.
Thanks to the Beijing Genomics Institute for providing these data.