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%

- Detection: Percentage of SNPs that are covered by at least five sequencing reads.

- Concordance: Percentage of detected SNPs that matched the HapMap (HapMap Public Release #27; merged II + III) genotype. Due to the underrepresentation of barcode 4 (BC4) in the pools 770 and 792, the detection and concordance rates were lower (assigned in this Table with *).

- gDNA: genomic DNA; WGA: whole-genome amplification; emPCR: emulsion PCR; BC: barcode.

ElSharawy et al.

ElSharawy et al. BMC Genomics 2012 13:500   doi:10.1186/1471-2164-13-500

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