Strain ID Tool
Given a set of SNPs, this tool computes concordances to the 1135 strains and reports a ranking of the most similar strains.
Please upload a valid VCF file or try one of these demo SNP sets:
SNP set #1: random subset of ~64k high quality SNPs extracted from strain 5779 (called with SHORE).
SNP set #2: random subset of ~3k high quality SNPs extracted from strain 108 (called with SHORE).
Note: Only SNPs with a filter set to 'PASS' will be considered.
Strain ID Tool
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Strain ID Tool
Sum of Concordant SNPs: Top 10 Strains
Overlapping SNPs of the top 3 candidates
Details
Help
TBD
About
Strain ID Tool compares uploaded SNPs in VCF format to SNPs contained in strains of the 1135 set. As result, a ranking of the most similar strains is returned.
Credits
Web app and database development was done by Joffrey Fitz.
References
The 1001 Genomes Consortium (2015). 1135 sequenced natural inbred lines reveal the global pattern of polymorphism in Arabidopsis thaliana. Manuscript submitted for publication.
Pseudogenomes Download
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Strain ID Tool
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