1001Genomes Tools
  • Strain ID
  • About

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.

Uploading... 0% complete.
weigelworld.org | Datenschutzerklärung | Impressum

Strain ID Tool

Your job identification is .

Status:
weigelworld.org | Datenschutzerklärung | Impressum

Strain ID Tool

Sum of Concordant SNPs: Top 10 Strains

Overlapping SNPs of the top 3 candidates

Details

weigelworld.org | Datenschutzerklärung | Impressum

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.

weigelworld.org | Datenschutzerklärung | Impressum

Pseudogenomes Download

Something went wrong ...

Error:

Strain ID Tool

Something went wrong ...

Error: