Table 2.
Whole Exome Sequencing metrics from PICARD.
| Hybrid Selection Metrics/ Sample Info | P1-BM | P1-Nail | P2-PB | P2-Nail | P3-BM | P3-Nail | P4-PB | P4-Nail | P5-PB | P5-Nail |
|---|---|---|---|---|---|---|---|---|---|---|
| Ref genome | hg19 | hg19 | hg19 | hg19 | hg19 | hg19 | hg19 | hg19 | hg19 | hg19 |
| GENOME_SIZE | 3,101,804,741 | 3,101,804,741 | 3,101,804,741 | 3,101,804,741 | 3,101,804,741 | 3,101,804,741 | 3,101,804,741 | 3,101,804,741 | 3,101,804,741 | 3,101,804,741 |
| BAIT_TERRITORY | 54,098,923 | 54,098,923 | 54,098,923 | 54,098,923 | 54,098,923 | 54,098,923 | 54,098,923 | 54,098,923 | 54,098,923 | 54,098,923 |
| TARGET_TERRITORY | 35,495,642 | 35,495,642 | 35,495,642 | 35,495,642 | 35,495,642 | 35,495,642 | 35,495,642 | 35,495,642 | 35,495,642 | 35,495,642 |
| PF_UNIQUE_READS | 106,789,318 | 107,344,759 | 94,279,613 | 50,395,498 | 69,779,721 | 62,557,872 | 77,039,161 | 67,576,894 | 72,182,769 | 65,553,926 |
| PCT_PF_UQ_READS | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% |
| PCT_PF_UQ_READS_ALIGNED | 98.3% | 97.2% | 97.7% | 95.3% | 97.8% | 95.2% | 98.1% | 97.2% | 98.2% | 99.3% |
| MEAN_TARGET_COVERAGE (fold) | 79.68 | 74.24 | 93.42 | 46.92 | 32.26 | 31.12 | 74.84 | 32.84 | 78.21 | 62.74 |
| MEDIAN_TARGET_COVERAGE | 77 | 72 | 94 | 42 | 28 | 28 | 72 | 30 | 74 | 15 |
| FOLD_ENRICHMENT | 16.94 | 17.04 | 22.94 | 27.04 | 19.75 | 22.19 | 22.51 | 21.07 | 25.04 | 24.12 |
| ZERO_CVG_TARGETS_PCT | 1.6% | 0.8% | 1.9% | 2.2% | 6.2% | 2.9% | 2.2% | 3.4% | 1.8% | 21.0% |
| PCT_TARGET_BASES_20× | 87.0% | 91.6% | 86.8% | 69.4% | 58.2% | 60.4% | 83.2% | 61.0% | 84.6% | 48.6% |
| Alignment Summary Metrics | ||||||||||
| Total # of paired PF Reads | 106,789,318 | 107,344,759 | 94,279,613 | 50,395,498 | 69,779,721 | 62,557,872 | 77,039,161 | 67,576,894 | 72,182,769 | 65,553,926 |
| # of PF Reads aligned (to the Ref genome) | 104,974,657 | 104,325,201 | 92,111,167 | 48,019,798 | 68,231,575 | 59,539,607 | 75,591,666 | 65,685,799 | 70,875,401 | 65,097,422 |
| % of PF reads aligned (to the Ref genome) | 98.3% | 97.2% | 97.7% | 95.3% | 97.8% | 95.2% | 98.1% | 97.2% | 98.2% | 99.3% |
| PF_ALIGNED_BASES | 14,427,132,005 | 13,107,271,771 | 12,506,043,273 | 5,375,447,023 | 5,092,009,746 | 4,367,257,183 | 10,208,827,634 | 4,851,700,895 | 9,610,230,332 | 8,182,262,500 |
| PF_HQ_ALIGNED_READS | 100,823,219 | 99,200,185 | 88,407,559 | 44,853,721 | 64,978,905 | 55,761,327 | 72,476,022 | 62,059,678 | 68,327,276 | 62,267,394 |
| PF_HQ_ALIGNED_BASES | 13,937,375,831 | 12,567,096,599 | 12,092,852,199 | 5,127,395,157 | 4,863,529,709 | 4,118,092,143 | 9,863,025,210 | 4,604,831,212 | 9,319,611,775 | 7,885,746,592 |
| PF_HQ_ALIGNED_Q20_BASES | 12,525,100,793 | 11,286,362,421 | 10,946,285,477 | 4,783,558,180 | 4,682,608,199 | 3,973,604,910 | 8,910,130,015 | 4,441,395,882 | 8,462,020,636 | 7,380,096,882 |
| MEAN_READ_LENGTH | 142 | 131 | 141 | 118 | 75 | 74 | 141 | 75 | 141 | 131 |
| READS_ALIGNED_IN_PAIRS | 104,420,518 | 103,689,169 | 91,553,864 | 47,878,460 | 67,693,047 | 59,049,484 | 75,100,061 | 65,166,522 | 70,349,086 | 64,968,572 |
| PCT_READS_ALIGNED_IN_PAIRS | 99.5% | 99.4% | 99.4% | 99.7% | 99.2% | 99.2% | 99.3% | 99.2% | 99.3% | 99.8% |
| MEAN_INSERT_SIZE | 175 | 141 | 172 | 122 | 184 | 128 | 170 | 136 | 170 | 139 |
| PCT Duplicates | 19.3 | 28.8 | 41.7 | 49.1 | 45.7 | 44.5 | 38.3 | 43.8 | 39.3 | 56.0 |
Note that the metrics shown in Table 2 were calculated after PCR duplicates had been removed.