Selected article for: "accession number and genome sequence"
Author: Pandya, Gagan A.; Holmes, Michael H.; Sunkara, Sirisha; Sparks, Andrew; Bai, Yun; Verratti, Kathleen; Saeed, Kelly; Venepally, Pratap; Jarrahi, Behnam; Fleischmann, Robert D.; Peterson, Scott N.
Title: A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform
  • Document date: 2007_11_15
    • ID: 16tii0ha_50
    Snippet: We used the set of expected SNPs present in the SCHU S4 sample, relative to the LVS reference sequence, to parameterize and validate our filter algorithms. Consequently, the possibility of over-fitting of the parameters to one particular genome sequence cannot be ignored. However, the excellent performance of the filters on the LVS query sample argues against this possibility. Additional experiments with the recently available genome sequence of .....
    Document: We used the set of expected SNPs present in the SCHU S4 sample, relative to the LVS reference sequence, to parameterize and validate our filter algorithms. Consequently, the possibility of over-fitting of the parameters to one particular genome sequence cannot be ignored. However, the excellent performance of the filters on the LVS query sample argues against this possibility. Additional experiments with the recently available genome sequence of a clinical strain WY96-3418 (GenBank accession number CP000608) also support the robustness of the filter parameters chosen. We used the published sequence data to predict the expected SNP calls and validate our results for WY96-3418, in the same way as was done for SCHU S4. Our filters eliminated over 95% of the false-positive SNP calls and achieved a call accuracy rate of 99.995%, equivalent to a Phred quality score of 43 (Supplementary Table 4 ).

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