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Table 1 Sample throughput and sequence capacity- general sequencing and enrichment metrics

From: Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing

HapMap sample ID Sample type Library ID Reads Mapped On-target % ADoC C1 C20 Coverage 0.2X mean
NA12003 gDNA 759L 36,453,208 33.50% 65.30% 2,121 99.50% 98.00% 86.10%
  WGA 765L 42,752,716 36.30% 63.20% 2,588 99.60% 98.10% 86.40%
  gDNA-pB 770L_BC1 10,031,809 36.40% 64.10% 621 99.00% 96.50% 86.50%
  gDNA-pA 792L_BC1 5,221,822 31.60% 64.20% 280 98.40% 93.50% 85.70%
NA12004 gDNA 760L 39,005,646 31.00% 73.30% 2,356 99.40% 98.00% 86.30%
  WGA 766L 43,079,257 17.50% 64.40% 1,273 99.40% 97.20% 84.80%
  gDNA-pB 770L_BC2 3,272,424 39.30% 72.70% 249 98.30% 93.60% 87.10%
  gDNA-pA 792L_BC2 6,023,113 32.50% 72.90% 380 98.50% 94.60% 85.70%
NA10838 gDNA 761L 35,573,703 21.10% 66.00% 1,309 99.40% 97.50% 85.90%
  WGA 767L 43,140,968 30.60% 57.80% 2,014 99.60% 98.20% 86.50%
  gDNA-pB 770L_BC3 7,114,637 35.80% 67.50% 456 98.60% 95.30% 85.80%
  gDNA-pA 792L_BC3 6,587,601 34.00% 67.60% 401 98.60% 94.90% 85.80%
NA11829 gDNA 762L 39,864,620 29.20% 63.90% 1,961 99.60% 97.90% 85.50%
  gDNA-pB 770L_BC4* 638,985 36.40% 66.00% 41 95.40% 63.40% 84.60%
  gDNA-pA 792L_BC4* 677,767 28.50% 66.40% 34 94.50% 55.40% 84.90%
NA11830 gDNA 763L 38,654,830 34.10% 68.50% 2,404 99.70% 98.10% 85.80%
  gDNA-pB 770L_BC5 Insufficient amount of material to run sample
  gDNA-pA 792L_BC5 5,403,560 32.80% 68.10% 320 98.40% 94.10% 85.60%
NA10856 gDNA 764L 43,185,707 34.60% 61.10% 2,418 99.50% 98.00% 85.80%
  gDNA-pB 770L_BC6 9,255,333 36.30% 61.30% 545 98.90% 96.00% 85.90%
  gDNA-pA 792L_BC6 6,435,690 33.90% 62.00% 357 98.50% 94.40% 85.00%
Pooled Samples gDNA 768L_1 41,913,860 32.40% 67.00% 2,406 99.80% 98.30% 84.90%
  gDNA 768L_2 41,958,628 33.40% 66.70% 2,474 99.60% 98.30% 85.30%
  1. - Reads: Total sequencing reads per sample.
  2. - Mapped: Percentage of total reads that could be aligned to the human genome (hg18/NCBI).
  3. - On-Target: Percentage of mapped reads that align to the target regions.
  4. - ADoC: Average depth of coverage of target base.
  5. - C1: Percentage of target bases that are covered by at least one sequencing read.
  6. - C20: Percentage of target bases that are covered by at least 20 sequencing reads.
  7. - Coverage 0.2× Mean: Percentage of target bases that are covered by at least 0.2× of ADoC. Note that one barcode (BC4) was underrepresented (assigned with “*” in this Table; see also Results and Discussion sections).
  8. - gDNA: genomic DNA; WGA: whole-genome amplification; emPCR: emulsion PCR; BC: barcode.