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).
SNP names are of the format
- supercontig: Supercontig number from assembly
- contig: Contig number (within supercontig) from assembly
- position: Starting offset within Contig.[supercontig].[contig]
- type: S=Substitution, I=Insertion or D=Deletion
- strain: 1=Broiler, 2=Layer, 3=Silkie
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.
Users are free to use these data in scientific papers analyzing
particular genes, if the Beijing Genomics Institute (BGI) is
BGI and its collaborators reserve the right to publish the initial
analyses of these data, including but not restricted to the large-scale
identification of functional polymorphisms, evolutionary patterns and
signs of selection, correlations with known QTLs, utility of data for
genetic mapping purposes, etc.
Any redistribution of these data should carry this notice.