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cDNA analysis for GRC rare and mono bases

cDNA analysis for GRC rare and mono bases. Ancestral Allele Comparison. Process. Rare and mono variants analysed by the Ensembl Variant Effect Predictor (version 67)

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cDNA analysis for GRC rare and mono bases

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  1. cDNA analysis for GRC rare and mono bases

  2. Ancestral Allele Comparison

  3. Process • Rare and mono variants analysed by the Ensembl Variant Effect Predictor (version 67) • We excluded variants whose most severe consequence was INTERGENIC, INTRONIC, DOWNSTREAM, UPSTREAM, WITHIN NON CODING and NMD_TRANSCRIPT • Overlap of gene based consequences versus EnsemblcDNA database (version 67) • Exonerate Alignment between variant (plus 30bp either side) and cDNA

  4. Variant Consequences

  5. Breakdown of Rarer Consequences

  6. Sift and Polyphen results

  7. cDNA Alignment

  8. cDNA Alignment Results

  9. Take Home Messages • Majority of variants are Intergenic and Intronic • Of those with Gene overlap more of the sites have cDNA support for the alt rather than the ref base • All results are available on ftp ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20120803_grc_cdna_analysis/ • A list of sites which may need more investigation are highlighted in 20120807_sites_for_further_investigation.txt

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