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Table 3 Variant detection rate and concordance1

From: Enrichment of sequencing targets from the human genome by solution hybridization

   Microarray SNPs2 Variant detection rate (%) Variant concordance3 (%) Number of discordant SNPs
Sample Replicate On target On or near target On target On or near target On target On or near target On target On or near target
NA15510 Capture 1 4,062 6,682 93.5 76.4 99.7 99.6 10 20
NA15510 Capture 2 4,062 6,682 93.7 75.2 99.8 99.8 8 10
HE00069 Capture 1 4,055 6,675 93.0 77.7 99.5 99.5 19 27
HE00069 Capture 2 4,055 6,675 93.4 77.4 99.6 99.6 14 22
  Average 4,059 6,679 93.4 76.7 99.7 99.6 13 20
  1. 1Only variant bases with an MAQ quality score of 30 or greater are included in this table.
  2. 2Number of microarray genotypes in the on-target sequences or in the on or near (target ± 150 bp) target sequences.
  3. 3Number of genotypes that match between sequence and microarray genotype divided by total comparisons.