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. 2017 Oct 24;4:170157. doi: 10.1038/sdata.2017.157

Table 3. Sequencing quality metrics for sequenced cell line.

Tissue External ID Sample name (.fastq) Total reads Total alignments Aligned Total unaligned Unaligned Total unique Unique Total non-unique Non-unique Coverage Avg. coverage depth Avg. length Avg. quality %GC
Breast BT-549 MX1381-C9C07ANXX-1-CACTGT 26,779,757 20,087,593 74.84% 6,738,932 25.16% 19,994,122 74.66% 46,703 0.17% 0.62% 23.36 22.33 33.02 47.70%
  HS-578T MX1383-C9C07ANXX-3-GGGGTT 24,961,809 20,875,168 83.42% 4,137,590 16.58% 20,773,358 83.22% 50,861 0.20% 0.35% 41.95 22.13 34.19 45.13%
  MCF-7 MX1384-C9C07ANXX-4-CTGGGT 43,741,142 32,170,069 73.27% 11,690,617 26.73% 31,931,263 73.00% 119,262 0.27% 0.81% 28.46 22.27 33.55 42.37%
  MDA-MB-231 MX1384-C9C07ANXX-4-GCCGGT 16,798,227 11,552,251 68.68% 5,261,551 31.32% 11,521,123 68.59% 15,553 0.09% 0.43% 19.43 22.45 33.25 46.01%
  T-47D MX1387-C9C07ANXX-7-CTAAGG 14,269,847 9,004,918 63.04% 5,274,372 36.96% 8,986,041 62.97% 9,434 0.07% 0.48% 13.58 22.4 32.16 47.83%
CNS SF-268 MX1386-C9C07ANXX-6-TAGTTG 35,537,775 32,273,096 90.47% 3,385,641 9.53% 32,031,463 90.13% 120,671 0.34% 0.28% 84.29 22.35 34.68 46.13%
  SF-295 MX1386-C9C07ANXX-6-CCGGTG 26,519,319 23,694,543 89.10% 2,890,215 10.90% 23,563,806 88.86% 65,298 0.25% 0.24% 70.66 22.39 34.43 42.31%
  SF-539 MX1386-C9C07ANXX-6-ATCGTG 25,500,558 23,012,418 90.00% 2,549,670 10.00% 22,889,448 89.76% 61,440 0.24% 0.25% 65.79 22.25 34.49 46.43%
  SNB-19 MX1387-C9C07ANXX-7-GCGTGG 32,717,872 21,567,743 65.75% 11,204,285 34.25% 21,459,531 65.59% 54,056 0.17% 0.85% 18.3 22.44 32.24 43.60%
  SNB-75 MX1387-C9C07ANXX-7-CATGGG 12,680,815 7,882,308 62.10% 4,805,816 37.90% 7,867,693 62.04% 7,306 0.06% 0.37% 15.13 22.2 32.05 45.20%
  U251 MX1387-C9C07ANXX-7-ATTCCG 20,845,308 13,006,365 62.30% 7,858,915 37.70% 12,966,435 62.20% 19,958 0.10% 0.58% 16.29 22.47 32.17 43.76%
Colon COLO 205 MX1381-C9C07ANXX-1-TCAAGT 18,351,752 13,907,298 75.66% 4,466,918 24.34% 13,862,401 75.54% 22,433 0.12% 0.44% 22.77 22.23 33.19 45.58%
  HCC2998 MX1382-C9C07ANXX-2-GTAGCC 22,418,943 16,741,250 74.53% 5,710,380 25.47% 16,675,921 74.38% 32,642 0.15% 0.88% 13.4 21.83 32.83 47.12%
  HCT-116 MX1382-C9C07ANXX-2-TACAAG 19,321,624 13,822,479 71.42% 5,521,561 28.58% 13,777,662 71.31% 22,401 0.12% 0.54% 18.43 22.23 33.06 46.02%
  HCT-15 MX1382-C9C07ANXX-2-ATGTTT 22,372,577 15,816,346 70.57% 6,585,278 29.43% 15,758,281 70.44% 29,018 0.13% 0.62% 18.15 22.24 32.92 46.00%
  HT-29 MX1383-C9C07ANXX-3-CAAGTT 43,295,013 36,704,351 84.42% 6,746,834 15.58% 36,392,459 84.06% 155,720 0.36% 0.64% 40.79 22.23 34.19 45.58%
  KM12 MX1383-C9C07ANXX-3-GTCCTT 21,097,776 17,022,531 80.52% 4,108,873 19.48% 16,955,321 80.37% 33,582 0.16% 0.41% 29.68 22.35 34.03 46.33%
  SW-620 MX1387-C9C07ANXX-7-TTGCGG 34,094,755 22,349,352 65.38% 11,803,916 34.62% 22,232,420 65.21% 58,419 0.17% 0.92% 17.57 22.46 32.21 46.44%
Leukemia CCRF-CEM MX1381-C9C07ANXX-1-GATCTG 16,675,728 12,545,480 75.12% 4,148,470 24.88% 12,509,054 75.01% 18,204 0.11% 0.40% 22.55 22.48 33.4 49.05%
  HL-60(TB) MX1382-C9C07ANXX-2-TGCTTT 14,448,374 9,588,877 66.29% 4,870,207 33.71% 9,567,467 66.22% 10,700 0.07% 0.51% 13.5 22.12 32.72 49.74%
  K-562 MX1383-C9C07ANXX-3-TCGCTT 35,495,593 28,500,403 80.03% 7,089,711 19.97% 28,311,603 79.76% 94,279 0.27% 0.60% 34.46 22.43 34.08 48.92%
  MOLT-4 MX1384-C9C07ANXX-4-GAGAGT 17,384,261 12,413,016 71.30% 4,989,141 28.70% 12,377,237 71.20% 17,883 0.10% 0.49% 18.25 22.49 33.61 48.27%
  RPMI 8226 MX1385-C9C07ANXX-5-AGGAAT 17,460,565 14,241,842 81.43% 3,242,340 18.57% 14,194,637 81.30% 23,588 0.14% 0.46% 22.37 22.47 34.06 48.91%
  SR MX1387-C9C07ANXX-7-CCACTC 12,064,850 6,751,739 55.92% 5,318,416 44.08% 6,741,131 55.87% 5,303 0.04% 0.48% 10.23 22.48 31.62 47.70%
Melanoma LOX-IMVI MX1383-C9C07ANXX-3-CCTATT 31,657,831 25,924,121 81.64% 5,812,011 18.36% 25,767,653 81.39% 78,167 0.25% 0.47% 39.9 22.38 34.1 45.79%
  M14 MX1383-C9C07ANXX-3-GTTTGT 16,456,810 13,115,289 79.57% 3,361,434 20.43% 13,075,479 79.45% 19,897 0.12% 0.32% 29.6 22.45 34.08 47.29%
  MALME-3M MX1383-C9C07ANXX-3-AGATGT 97,640 42,454 43.48% 55,187 56.52% 42,452 43.48% 1 0% 0.01% 4.85 22.33 29.76 46.02%
  MDA-MB-435 MX1384-C9C07ANXX-4-TATCGT 16,462,112 11,741,084 71.22% 4,736,983 28.78% 11,709,183 71.13% 15,946 0.10% 0.50% 16.9 22.36 33.4 47.73%
  SK-MEL-2 MX1386-C9C07ANXX-6-TGAGTG 30,951,870 27,402,647 88.25% 3,636,213 11.75% 27,228,840 87.97% 86,817 0.28% 0.32% 61.56 22.51 34.52 46.50%
  SK-MEL-28 MX1386-C9C07ANXX-6-CGCCTG 14,712,878 12,743,244 86.48% 1,988,450 13.52% 12,705,638 86.36% 18,790 0.13% 0.22% 41.57 22.26 34.24 46.57%
  SK-MEL-5 MX1386-C9C07ANXX-6-GCCATG 12,394,333 10,855,860 87.48% 1,552,173 12.52% 10,828,474 87.37% 13,686 0.11% 0.19% 41.26 22.5 34.4 46.38%
  UACC-257 MX1388-C9C07ANXX-8-AGCTAG 46,062 9,213 20.00% 36,849 80.00% 9,213 20.00% 0 0% 0% 2.13 22.17 26.55 46.63%
  UACC-62 MX1388-C9C07ANXX-8-GTATAG 22,270,501 15,834,593 70.97% 6,465,114 29.03% 15,776,225 70.84% 29,162 0.13% 0.62% 18.26 22.24 32.7 46.13%
NSCLC A549 MX1381-C9C07ANXX-1-GCCTAA 24,542,337 18,533,593 75.35% 6,048,721 24.65% 18,453,696 75.19% 39,920 0.16% 0.53% 25.18 22.39 33.18 45.04%
  EKVX MX1382-C9C07ANXX-2-AAGCTA 18,358,000 13,056,340 71.01% 5,321,501 28.99% 13,016,669 70.90% 19,830 0.11% 0.46% 20.08 22.13 32.99 45.71%
  HOP 62 MX1382-C9C07ANXX-2-GCATTT 22,874,592 16,227,434 70.81% 6,678,209 29.19% 16,165,375 70.67% 31,008 0.14% 0.58% 19.83 22.18 32.86 45.15%
  HOP 92 MX1382-C9C07ANXX-2-CGTACG 16,671,005 11,307,213 67.74% 5,378,661 32.26% 11,277,492 67.65% 14,852 0.09% 0.49% 16.63 22.16 32.7 45.80%
  NCI-H226 MX1384-C9C07ANXX-4-TCTTCT 18,745,702 12,999,215 69.24% 5,766,399 30.76% 12,959,420 69.13% 19,883 0.11% 0.52% 17.92 22.38 33.28 47.25%
  NCI-H23 MX1384-C9C07ANXX-4-CTATCT 19,234,429 13,677,426 71.00% 5,578,694 29.00% 13,634,066 70.88% 21,669 0.11% 0.51% 19.47 22.44 33.36 48.52%
  NCI-H322M MX1384-C9C07ANXX-4-GATGCT 40,017,514 30,184,128 75.16% 9,938,560 24.84% 29,974,031 74.90% 104,923 0.26% 0.95% 22.98 22.47 33.58 45.76%
  NCI-H460 MX1385-C9C07ANXX-5-AGCGCT 12,712,247 9,871,928 77.57% 2,851,889 22.43% 9,848,794 77.47% 11,564 0.09% 0.32% 22.39 22.38 33.72 47.50%
  NCI-H522 MX1385-C9C07ANXX-5-CGGCCT 37,514,479 30,982,049 82.29% 6,643,642 17.71% 30,759,900 81.99% 110,937 0.30% 0.55% 40.76 22.53 34.02 44.85%
Ovarian IGR-OV1 MX1383-C9C07ANXX-3-AGTCTT 28,718,340 23,886,771 82.95% 4,897,725 17.05% 23,754,573 82.72% 66,042 0.23% 0.42% 41.25 22.41 34.16 46.10%
  NCI/ADR-RES MX1384-C9C07ANXX-4-ATCAGT 22,291,994 16,348,364 73.20% 5,974,630 26.80% 16,286,408 73.06% 30,956 0.14% 0.54% 21.99 22.37 33.49 47.02%
  OVCAR-3 MX1385-C9C07ANXX-5-AATTAT 29,981,152 25,036,208 83.26% 5,017,926 16.74% 24,890,371 83.02% 72,855 0.24% 0.46% 38.94 22.41 34.16 47.68%
  OVCAR-4 MX1385-C9C07ANXX-5-CCGTAT 28,168,179 22,957,608 81.29% 5,271,643 18.71% 22,835,575 81.07% 60,961 0.22% 0.43% 38.31 22.39 34.02 47.21%
  OVCAR-5 MX1385-C9C07ANXX-5-TAGGAT 24,989,662 20,898,933 83.43% 4,141,256 16.57% 20,797,961 83.23% 50,445 0.20% 0.40% 37.13 22.3 34.22 45.64%
  OVCAR-8 MX1385-C9C07ANXX-5-ATAGAT 21,340,411 17,484,019 81.76% 3,891,733 18.24% 17,413,389 81.60% 35,289 0.17% 0.35% 36.62 22.44 34.22 46.25%
  SK-OV-3 MX1386-C9C07ANXX-6-AAAATG 35,063,352 31,836,638 90.46% 3,344,843 9.54% 31,600,666 90.12% 117,843 0.34% 0.30% 76.21 22.49 34.54 46.04%
Prostate DU-145 MX1382-C9C07ANXX-2-CTGATC 42,719,250 30,543,575 71.24% 12,284,018 28.76% 30,327,141 70.99% 108,091 0.25% 1.01% 21.68 22.17 32.93 42.80%
  PC-3 MX1385-C9C07ANXX-5-GCTCAT 28,554,855 23,674,991 82.68% 4,944,659 17.32% 23,545,544 82.46% 64,652 0.23% 0.44% 38.54 22.42 34.15 46.08%
Renal 786-0 MX1381-C9C07ANXX-1-CGTGAT 28,239,458 21,417,620 75.65% 6,875,229 24.35% 21,310,920 75.47% 53,309 0.19% 0.53% 28.79 22.32 33.21 45.18%
  A498 MX1381-C9C07ANXX-1-ACATCG 23,983,341 18,160,244 75.56% 5,861,378 24.44% 18,083,724 75.40% 38,239 0.16% 0.49% 26.57 22.26 33.14 44.19%
  ACHN MX1381-C9C07ANXX-1-TGGTCA 26,253,335 20,447,816 77.70% 5,854,225 22.30% 20,350,495 77.52% 48,615 0.19% 0.50% 29.38 22.42 33.4 44.66%
  CAKI-1 MX1381-C9C07ANXX-1-ATTGGC 20,365,416 15,568,695 76.31% 4,825,051 23.69% 15,512,066 76.17% 28,299 0.14% 0.38% 29.39 22.37 33.42 44.53%
  RXF393 MX1386-C9C07ANXX-6-CTTTTG 29,863,988 26,677,423 89.05% 3,269,280 10.95% 26,512,156 88.78% 82,552 0.28% 0.34% 57.33 22.42 34.42 48.85%
  SN12C MX1387-C9C07ANXX-7-TGTTGG 23,377,833 15,428,844 65.88% 7,976,649 34.12% 15,373,563 65.76% 27,621 0.12% 0.67% 16.45 22.28 32.21 45.57%
  TK-10 MX1387-C9C07ANXX-7-TTCTCG 26,774,556 17,534,744 65.36% 9,275,498 34.64% 17,463,407 65.22% 35,651 0.13% 1.16% 10.66 21.92 31.69 49.55%
  UO-31 MX1388-C9C07ANXX-8-TCTGAG 12,737,055 8,368,476 65.64% 4,376,740 34.36% 8,352,163 65.57% 8,152 0.06% 0.34% 17.82 22.44 32.53 45.42%
MEAN
 23,457,233 18,073,055 74.34% 5,429,370 25.66% 17,982,756 74.18% 45,107 0.16% 0.49% 29 22.34 33.25 46.26%
Standard Deviation 9,294,225 7,957,399 11.69% 2,519,478 11.69% 7,888,112 11.63% 35,871 0.08% 0.22% 17 0.14 1.28 1.64%