Table 3 Experimental duplicate layout, read and coverage statistics
From: Target enrichment using parallel nanoliter quantitative PCR amplification
Sample | Number of PCR replicates | Total number of reads | Mapped | On target | PCR duplicates | Amplicon | Exon | ||
|---|---|---|---|---|---|---|---|---|---|
Mean coverage | Standard deviation | Mean coverage | Standard deviation | ||||||
Normal1-duplicate-B | 2 | 951169 | 97.7% | 79.0% | 15.6% | 542.7 | 334.9 | 427.9 | 409.4 |
BT-549 | 2 | 1031471 | 97.4% | 77.9% | 16.6% | 567.7 | 365.2 | 451.1 | 436.8 |
CCRF-CEM | 2 | 894547 | 97.7% | 76.4% | 15.2% | 498.4 | 356.9 | 403.3 | 413.9 |
HCT-15 | 2 | 826606 | 97.7% | 80.3% | 14.0% | 486.5 | 327.9 | 384.1 | 387.4 |
MOLT-4 | 2 | 1271883 | 97.9% | 77.3% | 17.2% | 747.0 | 460.3 | 589.9 | 561.2 |
HCT116 | 2 | 1384151 | 97.7% | 72.0% | 21.0% | 724.4 | 524.5 | 589.1 | 609.5 |
Normal1-duplicate-A | 2 | 1608833 | 97.9% | 74.3% | 20.6% | 877.3 | 536.2 | 692.3 | 658.2 |
SN12C | 2 | 472237 | 97.8% | 84.7% | 9.8% | 294.1 | 199.9 | 233.5 | 233.6 |
IGROV-1 | 2 | 672337 | 97.8% | 79.7% | 11.6% | 404.9 | 281.6 | 325.8 | 329.2 |
DU-145 | 2 | 723007 | 97.8% | 82.1% | 12.3% | 434.7 | 273.1 | 346.9 | 332.1 |
MDA-MB-231 | 2 | 769668 | 97.7% | 81.2% | 13.2% | 461.8 | 315.7 | 367.6 | 373.4 |
OVCAR-5 | 2 | 659926 | 97.3% | 81.1% | 13.1% | 386.5 | 293.4 | 308.1 | 332.7 |
786-O | 2 | 1167234 | 97.9% | 79.1% | 17.2% | 684.6 | 463.9 | 543.9 | 549.2 |
MCF7-B | 2 | 1053960 | 97.8% | 77.8% | 17.3% | 588.1 | 398.9 | 472.1 | 473.4 |
PC3 | 2 | 566416 | 97.8% | 79.9% | 11.5% | 329.9 | 252.1 | 267.3 | 287.9 |
MCF7-A | 2 | 1299077 | 97.6% | 76.0% | 19.3% | 703.5 | 465.2 | 569.0 | 558.0 |
RPMI-8226 | 1 | 1037872 | 97.5% | 77.2% | 16.9% | 575.4 | 394.6 | 462.1 | 461.8 |
Normal2-singleton-A | 1 | 806612 | 97.7% | 79.9% | 14.5% | 461.2 | 296.8 | 367.2 | 355.5 |
MCF7 | 1 | 1193431 | 97.6% | 75.3% | 18.2% | 647.8 | 441.9 | 515.4 | 513.5 |
Normal1-singleton-A | 1 | 1227019 | 97.9% | 74.7% | 17.3% | 688.5 | 450.0 | 543.0 | 533.9 |
Normal2-singelton-B | 1 | 571558 | 97.7% | 82.8% | 11.3% | 340.9 | 227.4 | 274.5 | 268.0 |
HT-29 | 1 | 578229 | 97.8% | 81.7% | 11.6% | 340.1 | 243.2 | 273.1 | 280.7 |
Normal1-singleton-B | 1 | 1070055 | 97.8% | 75.9% | 15.6% | 615.2 | 393.4 | 488.2 | 472.0 |
ACHN | 1 | 853092 | 97.8% | 79.2% | 14.9% | 486.6 | 327.2 | 387.2 | 384.2 |
Mean | 945432.9 | 97.7% | 78.6% | 15.2% | 537.0 | 359.3 | 428.4 | 425.6 | |
Stadard deviation | 296401.9 | 0.1% | 3.0% | 3.0% | 153.0 | 94.2 | 121.2 | 115.0 | |