Table 1.
Sample throughput and sequence capacity- general sequencing and enrichment metrics
| 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% | |
- Reads: Total sequencing reads per sample.
- Mapped: Percentage of total reads that could be aligned to the human genome (hg18/NCBI).
- On-Target: Percentage of mapped reads that align to the target regions.
- ADoC: Average depth of coverage of target base.
- C1: Percentage of target bases that are covered by at least one sequencing read.
- C20: Percentage of target bases that are covered by at least 20 sequencing reads.
- 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).
- gDNA: genomic DNA; WGA: whole-genome amplification; emPCR: emulsion PCR; BC: barcode.