## Description

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 snp.[supercontig].[contig].[position].[type].[strain]:

- 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

## Methods

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.

## Credits

Thanks to the Beijing Genomics Institute for providing these data.

## Terms of Use

1. Users are free to use these data in scientific papers analyzing particular genes, if the Beijing Genomics Institute (BGI) is acknowledged.
2. 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.
3. Any redistribution of these data should carry this notice.