Online-Only Table 1.
Whole Genome Sequencing (WGS) data sets for fresh DNA extracted from HCC1395BL and HCC1395 cell lines.
| Sample ID | Sample | Biosample | Platform | Machine model | library Protocol (Input amount) | Total Reads | Total Reads After Trimming | Percent Total Reads after Trimming | Total Mapped Reads | Percent Total Mapped Reads (Trimmed) | Percent Non-duplicated Reads (Mapped Trimmed) | Mean Coverage Depth | Mean Coverage Depth SD | Percent of Coverage > = 5X | Percent of Coverage > = 15X | Percent of Coverage > = 30X | Percent GC | Median Insert Size |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| WGS_IL_N_1 | HCC1395BL | Fresh cells | HiSeq | HiSeq 3000/4000 | TruSeq DNA PCR Free (1000 ng) | 1,922,974,720 | 1,921,659,788 | 99.93 | 1,913,037,464 | 99.55 | 95.20 | 58.98 | 351.92 | 93.68 | 93.12 | 87.97 | 39.70 | 419 |
| WGS_IL_N_2 | HCC1395BL | Fresh cells | HiSeq | HiSeq 3000/4000 | TruSeq DNA PCR Free (1000 ng) | 1,552,485,544 | 1,551,295,230 | 99.92 | 1,546,324,619 | 99.68 | 93.78 | 50.04 | 370.95 | 93.64 | 92.41 | 82.08 | 39.22 | 393 |
| WGS_IL_N_3 | HCC1395BL | Fresh cells | HiSeq | HiSeq 3000/4000 | TruSeq DNA PCR Free (1000 ng) | 1,672,746,794 | 1,672,206,086 | 99.97 | 1,664,765,047 | 99.56 | 94.50 | 50.79 | 384.54 | 93.66 | 92.53 | 82.59 | 39.18 | 402 |
| WGS_IL_T_1 | HCC1395 | Fresh cells | HiSeq | HiSeq 3000/4000 | TruSeq DNA PCR Free (1000 ng) | 2,152,864,926 | 2,151,176,006 | 99.92 | 2,141,479,936 | 99.55 | 95.11 | 67.00 | 292.90 | 93.05 | 92.38 | 86.88 | 39.90 | 417 |
| WGS_IL_T_2 | HCC1395 | Fresh cells | HiSeq | HiSeq 3000/4000 | TruSeq DNA PCR Free (1000 ng) | 1,742,944,436 | 1,741,213,400 | 99.90 | 1,735,985,947 | 99.70 | 92.73 | 56.10 | 288.78 | 92.99 | 91.40 | 80.83 | 39.63 | 395 |
| WGS_IL_T_3 | HCC1395 | Fresh cells | HiSeq | HiSeq 3000/4000 | TruSeq DNA PCR Free (1000 ng) | 1,745,338,388 | 1,744,749,370 | 99.97 | 1,737,271,357 | 99.57 | 93.05 | 53.38 | 289.37 | 93.00 | 91.22 | 78.86 | 39.40 | 401 |
| WGS_EA_N_1 | HCC1395BL | Fresh cells | HiSeq | HiSeq X10 | TruSeq DNA PCR Free (1000 ng) | 1,740,311,982 | 1,737,882,004 | 99.86 | 1,731,224,725 | 99.62 | 87.04 | 64.22 | 337.23 | 93.65 | 93.31 | 90.53 | 40.05 | 412 |
| WGS_EA_T_1 | HCC1395 | Fresh cells | HiSeq | HiSeq X10 | TruSeq DNA PCR Free (1000 ng) | 1,885,118,894 | 1,883,492,596 | 99.91 | 1,874,626,618 | 99.53 | 92.32 | 63.85 | 246.40 | 93.03 | 92.48 | 87.75 | 40.20 | 422 |
| WGS_NC_N_1 | HCC1395BL | Fresh cells | HiSeq | HiSeq 3000/4000 | TruSeq DNA PCR Free (1000 ng) | 1,232,116,762 | 1,231,187,894 | 99.93 | 1,226,338,013 | 99.61 | 96.27 | 42.69 | 52.04 | 99.09 | 92.12 | 79.19 | 42.95 | 417 |
| WGS_NC_T_1 | HCC1395 | Fresh cells | HiSeq | HiSeq 3000/4000 | TruSeq DNA PCR Free (1000 ng) | 1,202,406,138 | 1,201,304,904 | 99.91 | 1,196,430,615 | 99.59 | 96.53 | 41.61 | 44.76 | 98.84 | 89.65 | 67.71 | 43.15 | 408 |
| WGS_LL_N_1 | HCC1395BL | Fresh cells | HiSeq | HiSeq 4000 | TruSeq DNA PCR Free (1000 ng) | 1,267,721,898 | 1,267,074,486 | 99.95 | 1,260,762,149 | 99.50 | 79.06 | 48.62 | 272.02 | 93.57 | 87.36 | 50.48 | 39.95 | 377 |
| WGS_LL_T_1 | HCC1395 | Fresh cells | HiSeq | HiSeq 4000 | TruSeq DNA PCR Free (1000 ng) | 1,248,345,468 | 1,247,771,438 | 99.95 | 1,240,175,659 | 99.39 | 79.82 | 47.80 | 196.07 | 92.89 | 80.01 | 35.94 | 40.20 | 372 |
| WGS_NV_N_1 | HCC1395BL | Fresh cells | HiSeq | HiSeq 4000 | TruSeq DNA PCR Free (1000 ng) | 2,737,041,074 | 2,736,265,592 | 99.97 | 2,725,324,100 | 99.60 | 93.22 | 93.15 | 555.75 | 93.72 | 93.51 | 92.88 | 40.03 | 400 |
| WGS_NV_N_2 | HCC1395BL | Fresh cells | HiSeq | HiSeq 4000 | TruSeq DNA PCR Free (1000 ng) | 2,755,558,524 | 2,753,791,014 | 99.94 | 2,743,237,055 | 99.62 | 93.17 | 95.22 | 557.97 | 93.72 | 93.51 | 92.91 | 39.98 | 390 |
| WGS_NV_N_3 | HCC1395BL | Fresh cells | HiSeq | HiSeq 4000 | TruSeq DNA PCR Free (1000 ng) | 2,765,895,594 | 2,764,785,302 | 99.96 | 2,752,475,146 | 99.56 | 92.14 | 94.43 | 555.64 | 93.72 | 93.51 | 92.90 | 39.96 | 395 |
| WGS_NV_T_1 | HCC1395 | Fresh cells | HiSeq | HiSeq 4000 | TruSeq DNA PCR Free (1000 ng) | 2,708,598,970 | 2,706,761,164 | 99.93 | 2,695,472,614 | 99.58 | 92.77 | 92.97 | 436.57 | 93.08 | 92.81 | 91.27 | 40.18 | 404 |
| WGS_NV_T_2 | HCC1395 | Fresh cells | HiSeq | HiSeq 4000 | TruSeq DNA PCR Free (1000 ng) | 2,752,035,508 | 2,751,442,992 | 99.98 | 2,741,523,523 | 99.64 | 92.23 | 95.13 | 496.20 | 93.08 | 92.82 | 91.42 | 40.18 | 394 |
| WGS_NV_T_3 | HCC1395 | Fresh cells | HiSeq | HiSeq 4000 | TruSeq DNA PCR Free (1000 ng) | 2,752,204,218 | 2,751,260,128 | 99.97 | 2,741,889,519 | 99.66 | 91.95 | 92.97 | 425.71 | 93.08 | 92.81 | 91.24 | 40.2 | 387 |
| WGS_FD_N_1 | HCC1395BL | Fresh cells | HiSeq | HiSeq X10 | TruSeq DNA PCR Free (1000 ng) | 1,140,214,238 | 1,139,328,958 | 99.92 | 1,135,160,204 | 99.63 | 92.15 | 42.43 | 219.92 | 93.56 | 92.44 | 82.02 | 40.15 | 367 |
| WGS_FD_N_2 | HCC1395BL | Fresh cells | HiSeq | HiSeq X10 | TruSeq DNA PCR Free (1000 ng) | 1,197,153,800 | 1,196,576,644 | 99.95 | 1,192,633,894 | 99.67 | 93.15 | 44.46 | 237.23 | 93.57 | 92.63 | 83.31 | 40.06 | 371 |
| WGS_FD_N_3 | HCC1395BL | Fresh cells | HiSeq | HiSeq X10 | TruSeq DNA PCR Free (1000 ng) | 1,174,631,698 | 1,174,023,848 | 99.95 | 1,170,212,823 | 99.68 | 92.75 | 43.43 | 230.61 | 93.57 | 92.55 | 82.72 | 40.1 | 368 |
| WGS_FD_T_1 | HCC1395 | Fresh cells | HiSeq | HiSeq X10 | TruSeq DNA PCR Free (1000 ng) | 1,100,936,840 | 1,100,540,416 | 99.96 | 1,096,693,277 | 99.65 | 91.24 | 41.16 | 155.16 | 92.88 | 90.27 | 69.33 | 40.34 | 377 |
| WGS_FD_T_2 | HCC1395 | Fresh cells | HiSeq | HiSeq X10 | TruSeq DNA PCR Free (1000 ng) | 1,136,080,154 | 1,135,450,092 | 99.95 | 1,131,808,658 | 99.68 | 91.65 | 43.07 | 160.70 | 92.88 | 90.65 | 72.60 | 40.43 | 375 |
| WGS_FD_T_3 | HCC1395 | Fresh cells | HiSeq | HiSeq X10 | TruSeq DNA PCR Free (1000 ng) | 1,166,219,086 | 1,165,667,134 | 99.95 | 1,162,681,088 | 99.74 | 89.02 | 44.95 | 171.40 | 92.89 | 90.90 | 75.11 | 40.33 | 371 |
| WGS_NS_N_1 | HCC1395BL | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,406,727,868 | 1,404,557,816 | 99.85 | 1,400,188,308 | 99.69 | 92.63 | 45.95 | 262.43 | 93.61 | 92.86 | 84.87 | 41.26 | 423 |
| WGS_NS_N_2 | HCC1395BL | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,505,296,280 | 1,504,606,110 | 99.95 | 1,497,164,368 | 99.51 | 93.97 | 41.48 | 215.63 | 93.63 | 92.53 | 82.24 | 40.86 | 400 |
| WGS_NS_N_3 | HCC1395BL | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,357,261,200 | 1,357,106,672 | 99.99 | 1,350,908,040 | 99.54 | 94.72 | 40.61 | 216.19 | 93.61 | 92.37 | 81.33 | 41.20 | 463 |
| WGS_NS_N_4 | HCC1395BL | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,367,955,412 | 1,367,339,034 | 99.96 | 1,362,514,522 | 99.65 | 94.13 | 41.75 | 228.73 | 93.61 | 92.54 | 82.51 | 41.11 | 419 |
| WGS_NS_N_5 | HCC1395BL | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,501,530,522 | 1,501,116,932 | 99.97 | 1,495,542,591 | 99.63 | 93.60 | 45.91 | 252.24 | 93.63 | 92.91 | 84.98 | 41.15 | 416 |
| WGS_NS_N_6 | HCC1395BL | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,564,194,248 | 1,563,842,202 | 99.98 | 1,559,297,663 | 99.71 | 91.12 | 51.52 | 285.71 | 93.63 | 93.13 | 87.07 | 41.23 | 413 |
| WGS_NS_N_7 | HCC1395BL | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,283,402,840 | 1,282,990,744 | 99.97 | 1,278,660,640 | 99.66 | 92.62 | 41.37 | 265.40 | 93.59 | 92.46 | 82.12 | 41.21 | 410 |
| WGS_NS_N_8 | HCC1395BL | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,462,304,546 | 1,461,608,958 | 99.95 | 1,454,550,980 | 99.52 | 94.39 | 40.66 | 209.18 | 93.62 | 92.41 | 81.52 | 40.93 | 399 |
| WGS_NS_N_9 | HCC1395BL | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,470,980,018 | 1,470,257,498 | 99.95 | 1,463,536,841 | 99.54 | 94.01 | 40.94 | 209.21 | 93.63 | 92.45 | 81.76 | 40.90 | 401 |
| WGS_NS_T_1 | HCC1395 | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,695,377,648 | 1,693,184,204 | 99.87 | 1,688,102,934 | 99.70 | 91.64 | 55.97 | 235.94 | 93.00 | 92.10 | 85.08 | 41.46 | 422 |
| WGS_NS_T_2 | HCC1395 | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,261,325,698 | 1,260,860,796 | 99.96 | 1,254,572,158 | 99.50 | 94.60 | 34.93 | 136.34 | 92.90 | 88.65 | 56.06 | 41.20 | 401 |
| WGS_NS_T_3 | HCC1395 | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,417,458,666 | 1,417,283,958 | 99.99 | 1,411,500,925 | 99.59 | 94.34 | 42.23 | 186.34 | 92.97 | 90.56 | 70.59 | 41.30 | 481 |
| WGS_NS_T_4 | HCC1395 | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,842,018,210 | 1,839,790,050 | 99.88 | 1,832,403,023 | 99.60 | 93.14 | 56.30 | 224.01 | 93.03 | 92.17 | 85.38 | 41.40 | 424 |
| WGS_NS_T_5 | HCC1395 | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,252,160,470 | 1,251,737,302 | 99.97 | 1,247,854,937 | 99.69 | 93.80 | 38.70 | 164.96 | 92.92 | 89.82 | 64.15 | 41.39 | 416 |
| WGS_NS_T_6 | HCC1395 | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,708,185,366 | 1,707,737,216 | 99.97 | 1,702,648,733 | 99.70 | 91.74 | 56.14 | 253.64 | 93.01 | 92.13 | 85.25 | 41.40 | 416 |
| WGS_NS_T_7 | HCC1395 | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,565,451,318 | 1,565,121,762 | 99.98 | 1,560,619,578 | 99.71 | 92.10 | 51.27 | 245.10 | 92.99 | 91.78 | 82.23 | 41.36 | 407 |
| WGS_NS_T_8 | HCC1395 | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,228,386,838 | 1,227,945,398 | 99.96 | 1,223,091,592 | 99.61 | 94.87 | 33.97 | 133.30 | 92.89 | 88.27 | 53.79 | 41.22 | 391 |
| WGS_NS_T_9 | HCC1395 | Fresh cells | NovaSeq | NovaSeq 6000 | TruSeq DNA PCR Free (1000 ng) | 1,368,505,404 | 1,367,590,086 | 99.93 | 1,361,753,887 | 99.57 | 94.29 | 38.33 | 148.99 | 92.94 | 89.80 | 63.81 | 41.14 | 395 |
Libraries were made from TruSeq DNA PCR Free (1000 ng) library protocol and sequenced by six sequencing centers on Illumina HiSeq 3000/4000, HiSeq X10 and NovaSeq 6000 for cross-site comparision.