Table 2 Variant detection and concordance- SNP concordance with HapMap genotypes
HapMap sample ID | DNA type | Library ID | Detection | Concordance | Homozygous | Heterozygous | SNPs with genotypes | SNPs not detected | False negative detection rate |
|---|---|---|---|---|---|---|---|---|---|
NA12003 | gDNA | 759L | 98.20% | 100.00% | 100.00% | 100.00% | 268 | 0 | 0,0% |
WGA | 765L | 97.80% | 100.00% | 100.00% | 100.00% | 268 | 0 | 0,0% | |
gDNA-pB | 770L_BC1 | 97.40% | 100.00% | 100.00% | 100.00% | 268 | 2 | 0,7% | |
gDNA-pA | 792L_BC1 | 96.50% | 100.00% | 100.00% | 100.00% | 268 | 5 | 1,9% | |
NA12004 | gDNA | 760L | 99.10% | 99.10% | 99.10% | 100.00% | 138 | 0 | 0,0% |
WGA | 766L | 99.10% | 99.10% | 99.10% | 100.00% | 138 | 1 | 0,7% | |
gDNA-pB | 770L_BC2 | 98.30% | 99.10% | 99.10% | 100.00% | 138 | 3 | 2,2% | |
gDNA-pA | 792L_BC2 | 97.40% | 99.10% | 99.10% | 100.00% | 138 | 3 | 2,2% | |
NA10838 | gDNA | 761L | 99.10% | 99.10% | 98.90% | 100.00% | 270 | 2 | 0,7% |
gDNA-pB | 770L_BC3 | 98.70% | 99.60% | 99.50% | 100.00% | 270 | 3 | 1,1% | |
gDNA-pA | 792L_BC3 | 98.30% | 99.60% | 99.50% | 100.00% | 270 | 2 | 0,7% | |
NA11829 | gDNA | 762L | 97.90% | 100.00% | 100.00% | 100.00% | 274 | 2 | 0,7% |
gDNA-pB | 770L_BC4 | 91.0%* | 99.50% | 99.50% | 100.00% | 274 | 43 | 15,7% | |
gDNA-pA | 792L_BC4 | 86.3%* | 100.00% | 100.00% | 100.00% | 274 | 55 | 20,1% | |
NA11830 | gDNA | 763L | 99.10% | 99.10% | 100.00% | 93.90% | 272 | 0 | 0,0% |
gDNA-pB | 770L_BC5 | Insufficient amount of material to run sample | |||||||
gDNA-pA | 792L_BC5 | 98.70% | 99.10% | 100.00% | 94.10% | 272 | 9 | 3,3% | |
NA10856 | gDNA | 764L | 99.60% | 99.60% | 100.00% | 97.40% | 273 | 1 | 0,4% |
gDNA-pB | 770L_BC6 | 98.70% | 99.10% | 99.50% | 97.30% | 273 | 3 | 1,1% | |
gDNA-pA | 792L_BC6 | 99.10% | 99.60% | 100.00% | 97.40% | 273 | 4 | 1,5% | |