Skip to main content

Table 1 Comparison of high confidence differences (HCDiffs) obtained from the CTRL and DEFA regions by sequence capture (SeqCap) with HapMap SNP genotypes.

From: Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing

  NA12716 NA12760   NA12716 NA12760
HapMap: heterozygous 244 263 SeqCap: heterozygous 711 646
SeqCap:    HapMap:   
homozygous for reference, no HCDiff 0 5 heterozygous 237 248
homozygous for reference 0 2 homozygous for variant 5 4
heterozygous 237 248 homozygous for reference 10 4
homozygous for variant 3 0    
not or poorly covered/alignment problem 4 8    
HapMap: homozygous for variant 254 217 SeqCap: homozygous for variant 526 468
SeqCap:    HapMap:   
homozygous for reference, no HCDiff 0 0 homozygous for variant 248 212
homozygous for reference 0 0 homozygous for reference 0 0
heterozygous 5 4 heterozygous 3 0
homozygous for variant 248 212    
not or poorly covered/alignment problem 1 1    
HapMap: homozygous for reference 839 842 SeqCap: homozygous for reference 151 137
SeqCap:    HapMap:   
homozygous for reference, no HCDiff 827 835 homozygous for variant 0 0
homozygous for reference 1 1 homozygous for reference 1 1
heterozygous 10 4 heterozygous 0 2
homozygous for variant 0 0    
not or poorly covered/alignment problem 1 2    
Sensitivity (heterozygous) 97,1% 94,3% Specificity (heterozygous) 94,0% 96,9%
Sensitivity (homozygous) 98,4% 99,0% Specificity (homozygous) 98,4% 98,6%
  1. The SeqCap HCDiffs were categorized according to the variant's allele frequency (VAF) with the human genome sequence (hg18) as reference allele: homozygous for reference (VAF 10-24%); heterozygous (VAF 25-75%); homozygous for variant (VAF 76-100%).