NIHMS1010189 Supplement Tables PDF
NIHMS1010189 Supplement Tables PDF
NIHMS1010189 Supplement Tables PDF
Feature
1) Distinct coverage
2) Distinct mutant fragments
3) Mutant allele frequency
4) Mean mapping quality of reads
5) Mean mapping quality of mutant fragments
6) Mean number of mismatches in mutant reads
7) Mean base quality of mutant bases at the variant position
8) Mean and standard deviation of variant’s distance to nearest end of read
9) Fisher’s Exact Test p-values comparing reference and alternate coverage in tumor to normal
10) Strand bias estimate
11) Length of adjacent polynucleotide tracts
12) GC% of adjacent sequence
13) DUST score of adjacent sequence
14) Percentage of adjacent bases identifed as repeats
15) Length of indel variant
hine learning algorithm
Relative Feature
Feature Type Importance
Tumor and Normal sequences 4.6%
Tumor and Normal sequences 1.7%
Tumor and Normal sequences 3.9%
Tumor and Normal sequences 1.2%
Tumor and Normal sequences 8.0%
Tumor and Normal sequences 1.8%
Tumor and Normal sequences 14.5%
Tumor sequence 5.2%
Tumor and Normal sequences 46.1%
Tumor sequence 5.9%
Reference genome 3.0%
Reference genome 0.4%
Reference genome 0.6%
Reference genome 0.2%
Tumor sequence 3.0%
Description
Count of unique sequenced fragments at a genomic position
Count of unique mutant fragments at a genomic position
Fraction of distinct mutant fragments: Distinct mutant fragments / Distinct coverage
Average alignment reported mapping quality score (MAPQ) for all reads at a genomic position
Average alignment reported mapping quality score (MAPQ) for mutant reads at a genomic position
Average edit distance per read compared to the reference at a genomic position
Average sequencer provided base quality at a genomic position
Measure of the cycle distance between a mutated genomic position and the end of read
Measure of statistical significance of measuring the mutant allele in tumor compared to matched normal sample or
Confidence bounds (50%) on the proportion of reads unique to the under-represented strand
Number of base pairs in homopolymer runs adjacent to a site up to a limit of 50 bp
Percentage of G+C bases out of total base pairs in a window +/- 50 bp of the genomic position
Low complexity score provided by DUST over a window +/- 50 bp of the genomic position
Fraction of base pairs identified as possible repetitive elements by Repeatmasker +/- 10 bp of the genomic position
Number of base pairs inserted or deleted. 0 for single base substitutions
r process matched normal
n
Table S2. Performance results for simulated low-purity tumors*
Cerebro MuTect1 MuT
Tumor
Sens PPV F1 FPR Sens PPV F1 FPR Sens PPV
1 100.0% 100.0% 100.0% 0.00 90.9% 94.5% 92.7% 0.14 96.2% 97.7%
2 100.0% 100.0% 100.0% 0.00 88.6% 86.7% 87.6% 0.35 95.5% 75.0%
3 100.0% 100.0% 100.0% 0.00 89.4% 87.4% 88.4% 0.33 93.2% 76.9%
4 100.0% 100.0% 100.0% 0.00 89.4% 88.7% 89.1% 0.29 97.7% 64.8%
5 100.0% 100.0% 100.0% 0.00 88.6% 86.0% 87.3% 0.37 97.0% 61.5%
6 100.0% 100.0% 100.0% 0.00 87.1% 86.5% 86.8% 0.35 93.9% 65.6%
*MAF in (10%-25%); Variants include 120 substitutions and 12 1-3bp indels. Sens=sensitivity, PPV=positive predictive v
Tect2 SomaticSniper Strelka VarDict
F1 FPR Sens PPV F1 FPR Sens PPV F1 FPR Sens PPV F1
96.9% 0.06 70.5% 36.8% 48.3% 3.11 97.7% 99.2% 98.5% 0.02 95.5% 74.6% 83.7%
84.0% 0.82 68.9% 37.9% 48.9% 2.90 96.2% 99.2% 97.7% 0.02 92.4% 68.5% 78.7%
84.2% 0.72 72.0% 39.4% 50.9% 2.84 94.7% 98.4% 96.5% 0.04 97.7% 65.2% 78.2%
77.9% 1.36 72.0% 38.3% 50.0% 2.97 96.2% 98.4% 97.3% 0.04 98.5% 69.5% 81.5%
75.3% 1.55 73.5% 37.7% 49.9% 3.11 96.2% 96.9% 96.6% 0.08 96.2% 73.0% 83.0%
77.3% 1.26 74.2% 39.4% 51.4% 2.93 97.0% 97.7% 97.3% 0.06 97.0% 71.5% 82.3%
value, F1=F-score for accuracy, FPR=False Positive Rate (per megabase pair)
VarScan2
FPR Sens PPV F1 FPR
0.84 99.2% 87.9% 93.2% 0.35
1.09 99.2% 67.9% 80.6% 1.21
1.34 98.5% 69.9% 81.8% 1.09
1.11 99.2% 67.9% 80.6% 1.21
0.91 97.7% 62.0% 75.9% 1.54
0.99 97.0% 66.0% 78.5% 1.28
Table S4. Sensitivity results by variant type of mutation calling meth
Variant Type Cerebro MuTect1 MuTect2 SomaticSniper
3bp DEL 99.3% N/A 86.6% N/A
2bp DEL 99.4% N/A 84.4% N/A
1bp DEL 99.3% N/A 95.3% N/A
SBS 99.5% 98.6% 96.0% 91.5%
1bp INS 99.5% N/A 96.0% N/A
2bp INS 99.5% N/A 95.7% N/A
3bp INS 99.5% N/A 95.5% N/A
*1000 of each variant type spiked in with MAF in (10%, 100%), in each of 6 normal cell lines. DEL=deletion; SBS
hods*
Strelka VarDict VarScan2
93.3% 99.5% 92.5%
92.5% 98.3% 92.3%
93.6% 97.6% 94.4%
97.7% 98.4% 95.5%
93.9% 98.5% 94.0%
92.4% 98.1% 93.2%
94.6% 99.4% 93.5%
S=single base substitution, INS=insertion.
Table S5. Sensitivity results for substitutions by MAF*
MAF Cerebro MuTect 1 MuTect 2 SomaticSniper Strelka VarDict VarScan2
10 - 25% 99.5% 97.6% 96.5% 76.1% 96.5% 96.8% 95.1%
25 - 50% 99.6% 99.2% 96.0% 99.7% 97.6% 99.6% 96.4%
> 50% 99.5% 99.2% 95.4% 99.7% 99.2% 99.0% 95.1%
*1000 variants spiked in each of 6 normal cell lines, uniformly distributed between MAF bins.
Table S6. Sensitivity results for insertion-deletions by MAF*
MAF Cerebro MuTect 1 MuTect 2 SomaticSniper Strelka VarDict VarScan2
10 - 25% 99.0% N/A 92.3% N/A 83.9% 96.8% 92.6%
25 - 50% 99.6% N/A 93.0% N/A 96.9% 99.4% 93.8%
> 50% 99.6% N/A 91.4% N/A 99.0% 99.5% 93.6%
*6000 variants spiked in each of 6 normal cell lines, uniformly distributed between MAF bins.
Table S7. Results of droplet digital PCR validation of somatic mutations
Yes
Yes
Yes Yes
Yes
Yes
Yes Yes
Yes
Yes
Yes
Yes Yes
Yes Yes
Yes
Yes Yes
Yes Yes
Yes
Yes Yes
Yes
Yes Yes
Yes
Yes Yes
Yes
ll sets shown here.
Table S8. Performance results for cell lines with validated somatic muta
Cerebro MuTect1 MuT
Tumor
Sens PPV F1 FPR Sens PPV F1 FPR Sens PPV
T1 99.0% 94.4% 96.7% 0.12 93.3% 97.6% 95.4% 0.04 94.3% 91.4%
T2 96.0% 97.9% 96.9% 0.02 90.0% 89.6% 89.8% 0.10 94.0% 92.2%
T3 96.0% 100.0% 98.0% 0.00 89.7% 97.1% 93.2% 0.06 92.1% 71.3%
T4 95.4% 98.1% 96.7% 0.04 79.8% 85.6% 82.6% 0.27 92.7% 64.5%
T5 99.0% 100.0% 99.5% 0.00 95.2% 92.6% 93.9% 0.14 93.3% 61.3%
*MAF in (20%-100%); Variants include substitutions and indels up to 100 bp in length. Sens=sensitivity, PPV=positive p
ations*
Tect2 SomaticSniper Strelka VarD
F1 FPR Sens PPV F1 FPR Sens PPV F1 FPR Sens PPV
92.8% 0.17 94.3% 31.9% 47.7% 3.98 95.2% 95.1% 95.2% 0.10 98.1% 65.1%
93.1% 0.08 90.0% 21.5% 34.7% 3.19 96.0% 92.2% 94.0% 0.08 100.0% 48.1%
80.4% 0.87 89.7% 40.7% 56.0% 3.03 92.9% 94.1% 93.5% 0.14 100.0% 72.6%
76.0% 1.05 86.2% 35.5% 50.3% 3.28 94.5% 87.6% 90.9% 0.27 100.0% 79.7%
74.0% 1.13 95.2% 39.1% 55.5% 2.78 95.2% 92.8% 94.0% 0.14 99.0% 74.4%
predictive value, F1=F-score for accuracy, FPR=False positive rate per megabase pair.
Dict VarScan2
F1 FPR Sens PPV F1 FPR
78.3% 1.03 93.3% 72.5% 81.6% 0.70
64.9% 1.05 96.0% 76.7% 85.3% 0.27
84.1% 0.89 89.7% 81.9% 85.6% 0.45
88.7% 0.52 88.1% 73.6% 80.2% 0.64
85.0% 0.66 92.4% 79.1% 85.2% 0.45
Table S9. Unique and shared mutation load results for Cerebro and
TCGAID TumorType Unique to Cerebro Shared Unique to TCGA
TCGA-05-4244 LUAD 9 155 21
TCGA-05-4249 LUAD 22 242 25
TCGA-05-4382 LUAD 118 933 162
TCGA-05-4384 LUAD 14 84 15
TCGA-05-4389 LUAD 14 140 18
TCGA-05-4395 LUAD 12 202 19
TCGA-05-4396 LUAD 82 46 188
TCGA-05-4397 LUAD 45 648 61
TCGA-05-4398 LUAD 55 388 94
TCGA-05-4403 LUAD 7 111 6
TCGA-05-4405 LUAD 27 209 62
TCGA-05-4410 LUAD 90 424 362
TCGA-05-4415 LUAD 8 160 16
TCGA-05-4417 LUAD 29 140 99
TCGA-05-4418 LUAD 24 197 27
TCGA-05-4420 LUAD 18 216 24
TCGA-05-4422 LUAD 1 28 5
TCGA-05-4425 LUAD 4 34 3
TCGA-05-4426 LUAD 5 33 7
TCGA-05-4430 LUAD 25 144 29
TCGA-05-4432 LUAD 40 328 83
TCGA-05-4433 LUAD 7 30 0
TCGA-05-4434 LUAD 3 25 4
TCGA-05-5420 LUAD 7 40 12
TCGA-05-5423 LUAD 9 120 12
TCGA-05-5425 LUAD 50 370 55
TCGA-05-5428 LUAD 27 278 38
TCGA-05-5429 LUAD 6 23 3
TCGA-17-Z000 LUAD 17 89 12
TCGA-17-Z001 LUAD 26 133 39
TCGA-17-Z002 LUAD 2 3 4
TCGA-17-Z003 LUAD 34 131 43
TCGA-17-Z004 LUAD 13 12 2
TCGA-17-Z005 LUAD 14 48 35
TCGA-17-Z007 LUAD 11 37 16
TCGA-17-Z009 LUAD 8 5 4
TCGA-17-Z010 LUAD 50 166 38
TCGA-17-Z011 LUAD 18 83 14
TCGA-17-Z013 LUAD 13 41 5
TCGA-17-Z014 LUAD 31 200 81
TCGA-17-Z015 LUAD 52 395 43
TCGA-17-Z016 LUAD 36 241 21
TCGA-17-Z017 LUAD 12 171 18
TCGA-17-Z019 LUAD 8 1 1
TCGA-17-Z020 LUAD 17 37 18
TCGA-17-Z022 LUAD 79 888 129
TCGA-17-Z025 LUAD 30 158 42
TCGA-17-Z026 LUAD 103 496 88
TCGA-17-Z031 LUAD 139 1708 255
TCGA-17-Z036 LUAD 7 59 5
TCGA-17-Z037 LUAD 18 92 13
TCGA-17-Z043 LUAD 20 144 20
TCGA-17-Z044 LUAD 20 85 6
TCGA-17-Z045 LUAD 50 494 68
TCGA-17-Z050 LUAD 19 97 30
TCGA-17-Z051 LUAD 13 89 64
TCGA-17-Z053 LUAD 30 157 75
TCGA-17-Z055 LUAD 42 185 99
TCGA-17-Z056 LUAD 28 185 60
TCGA-17-Z057 LUAD 27 265 38
TCGA-17-Z058 LUAD 9 40 48
TCGA-17-Z059 LUAD 14 104 23
TCGA-17-Z061 LUAD 15 126 15
TCGA-18-3407 LUSC 14 16 36
TCGA-18-3409 LUSC 104 983 1467
TCGA-18-3412 LUSC 65 40 65
TCGA-18-3415 LUSC 26 87 70
TCGA-18-3416 LUSC 28 99 177
TCGA-18-3421 LUSC 21 116 153
TCGA-18-4721 LUSC 15 109 20
TCGA-18-5592 LUSC 14 219 22
TCGA-18-5595 LUSC 13 165 17
TCGA-21-1070 LUSC 43 338 132
TCGA-21-1071 LUSC 30 90 28
TCGA-21-1077 LUSC 30 133 30
TCGA-21-5782 LUSC 26 298 34
TCGA-21-5784 LUSC 24 86 19
TCGA-21-5786 LUSC 15 305 30
TCGA-21-5787 LUSC 32 332 25
TCGA-22-0944 LUSC 6 81 10
TCGA-22-1002 LUSC 10 158 16
TCGA-22-1011 LUSC 5 66 8
TCGA-22-1012 LUSC 43 133 53
TCGA-22-1016 LUSC 62 147 137
TCGA-22-4591 LUSC 10 122 33
TCGA-22-4593 LUSC 14 142 14
TCGA-22-4595 LUSC 18 232 35
TCGA-22-4599 LUSC 27 278 18
TCGA-22-4601 LUSC 12 124 10
TCGA-22-4607 LUSC 3 35 3
TCGA-22-4613 LUSC 41 477 40
TCGA-22-5471 LUSC 16 164 17
TCGA-22-5472 LUSC 28 280 26
TCGA-22-5473 LUSC 34 589 44
TCGA-22-5474 LUSC 3 68 7
TCGA-22-5478 LUSC 20 133 12
TCGA-22-5480 LUSC 13 119 14
TCGA-22-5482 LUSC 10 124 10
TCGA-22-5485 LUSC 9 171 16
TCGA-22-5489 LUSC 21 179 19
TCGA-22-5491 LUSC 23 235 23
TCGA-22-5492 LUSC 16 168 24
TCGA-2F-A9KO BLCA 30 394 20
TCGA-2F-A9KP BLCA 3 117 7
TCGA-2F-A9KQ BLCA 4 59 0
TCGA-2F-A9KR BLCA 10 171 4
TCGA-2F-A9KT BLCA 8 310 11
TCGA-2F-A9KW BLCA 10 85 5
TCGA-2V-A95S LIHC 10 73 7
TCGA-2Y-A9GS LIHC 8 51 7
TCGA-2Y-A9GT LIHC 9 76 2
TCGA-2Y-A9GV LIHC 7 51 2
TCGA-2Y-A9GW LIHC 5 58 4
TCGA-2Y-A9GX LIHC 5 29 3
TCGA-2Y-A9GY LIHC 5 60 2
TCGA-2Y-A9GZ LIHC 7 78 1
TCGA-2Y-A9H0 LIHC 7 67 2
TCGA-2Y-A9H1 LIHC 8 106 9
TCGA-2Y-A9H2 LIHC 5 42 5
TCGA-2Y-A9H3 LIHC 16 100 7
TCGA-2Y-A9H4 LIHC 2 59 4
TCGA-2Y-A9H8 LIHC 7 59 3
TCGA-2Y-A9H9 LIHC 10 107 2
TCGA-2Y-A9HA LIHC 5 118 11
TCGA-2Y-A9HB LIHC 4 60 0
TCGA-33-4532 LUSC 36 240 44
TCGA-33-4538 LUSC 18 133 27
TCGA-33-4547 LUSC 9 140 12
TCGA-33-4566 LUSC 87 1061 97
TCGA-33-4582 LUSC 12 128 21
TCGA-33-4583 LUSC 33 413 69
TCGA-33-4586 LUSC 23 269 25
TCGA-33-6737 LUSC 28 344 26
TCGA-34-2596 LUSC 24 167 37
TCGA-34-2600 LUSC 19 269 26
TCGA-34-5231 LUSC 45 523 41
TCGA-34-5232 LUSC 9 94 48
TCGA-34-5234 LUSC 28 61 21
TCGA-34-5236 LUSC 21 106 22
TCGA-34-5239 LUSC 15 181 22
TCGA-34-5241 LUSC 9 112 13
TCGA-34-5927 LUSC 19 209 17
TCGA-34-5928 LUSC 20 222 16
TCGA-34-5929 LUSC 10 169 20
TCGA-35-3615 LUAD 7 92 4
TCGA-35-4123 LUAD 18 165 46
TCGA-35-5375 LUAD 31 332 35
TCGA-37-4135 LUSC 13 225 31
TCGA-37-4141 LUSC 14 257 42
TCGA-37-5819 LUSC 52 586 72
TCGA-38-4627 LUAD 1 10 5
TCGA-38-4628 LUAD 5 75 12
TCGA-38-4629 LUAD 19 194 33
TCGA-38-4630 LUAD 7 87 14
TCGA-38-4631 LUAD 81 561 52
TCGA-38-4632 LUAD 50 356 52
TCGA-38-6178 LUAD 8 33 2
TCGA-38-7271 LUAD 10 10 14
TCGA-38-A44F LUAD 2 1 1
TCGA-39-5016 LUSC 25 267 27
TCGA-39-5019 LUSC 11 110 17
TCGA-39-5021 LUSC 15 97 23
TCGA-39-5022 LUSC 11 58 14
TCGA-39-5024 LUSC 12 114 13
TCGA-39-5028 LUSC 13 84 7
TCGA-39-5029 LUSC 9 111 5
TCGA-39-5030 LUSC 26 56 19
TCGA-39-5031 LUSC 35 373 52
TCGA-39-5036 LUSC 10 177 19
TCGA-39-5037 LUSC 7 171 17
TCGA-39-5039 LUSC 19 97 20
TCGA-3K-AAZ8 LIHC 12 104 6
TCGA-43-2578 LUSC 30 181 87
TCGA-43-3394 LUSC 60 74 51
TCGA-43-3920 LUSC 74 116 108
TCGA-43-5668 LUSC 57 487 63
TCGA-43-6143 LUSC 19 252 20
TCGA-43-6647 LUSC 17 78 13
TCGA-43-6770 LUSC 20 144 23
TCGA-43-6771 LUSC 24 156 23
TCGA-44-2656 LUAD 90 479 164
TCGA-44-2657 LUAD 27 206 66
TCGA-44-2659 LUAD 70 273 88
TCGA-44-2661 LUAD 0 14 10
TCGA-44-2662 LUAD 50 107 35
TCGA-44-2665 LUAD 29 22 9
TCGA-44-2666 LUAD 8 16 3
TCGA-44-2668 LUAD 85 206 56
TCGA-44-3396 LUAD 19 103 7
TCGA-44-3398 LUAD 11 50 28
TCGA-44-3918 LUAD 148 465 224
TCGA-44-4112 LUAD 22 316 76
TCGA-44-5644 LUAD 73 725 124
TCGA-44-5645 LUAD 4 23 11
TCGA-44-6144 LUAD 13 169 18
TCGA-44-6145 LUAD 23 233 23
TCGA-44-6146 LUAD 4 25 9
TCGA-44-6147 LUAD 37 27 13
TCGA-44-6148 LUAD 0 4 0
TCGA-44-6774 LUAD 23 146 91
TCGA-44-6775 LUAD 8 11 33
TCGA-44-6776 LUAD 13 148 21
TCGA-44-6777 LUAD 25 94 148
TCGA-44-6778 LUAD 26 246 66
TCGA-44-6779 LUAD 13 71 9
TCGA-44-7659 LUAD 5 117 11
TCGA-44-7660 LUAD 18 241 21
TCGA-44-7661 LUAD 17 93 96
TCGA-44-7662 LUAD 40 417 34
TCGA-44-7667 LUAD 35 315 56
TCGA-44-7669 LUAD 28 366 25
TCGA-44-7670 LUAD 57 664 272
TCGA-44-7671 LUAD 20 171 21
TCGA-44-7672 LUAD 17 82 4
TCGA-44-8119 LUAD 49 469 63
TCGA-44-8120 LUAD 49 479 44
TCGA-44-A479 LUAD 14 174 23
TCGA-44-A47A LUAD 13 142 9
TCGA-44-A47B LUAD 6 34 1
TCGA-44-A47F LUAD 7 53 10
TCGA-44-A47G LUAD 6 26 2
TCGA-44-A4SS LUAD 32 277 33
TCGA-44-A4SU LUAD 8 91 11
TCGA-46-3765 LUSC 40 74 113
TCGA-46-3767 LUSC 55 31 65
TCGA-46-3768 LUSC 53 108 112
TCGA-46-3769 LUSC 75 352 373
TCGA-46-6025 LUSC 10 112 47
TCGA-46-6026 LUSC 12 178 9
TCGA-49-4486 LUAD 7 64 26
TCGA-49-4487 LUAD 43 154 38
TCGA-49-4488 LUAD 17 206 35
TCGA-49-4490 LUAD 4 21 1
TCGA-49-4494 LUAD 19 138 12
TCGA-49-4501 LUAD 5 24 4
TCGA-49-4506 LUAD 19 77 13
TCGA-49-4507 LUAD 17 127 21
TCGA-49-4510 LUAD 7 23 16
TCGA-49-4512 LUAD 5 21 2
TCGA-49-4514 LUAD 28 230 30
TCGA-49-6742 LUAD 17 174 12
TCGA-49-6743 LUAD 69 392 143
TCGA-49-6744 LUAD 19 66 51
TCGA-49-6745 LUAD 10 53 28
TCGA-49-6761 LUAD 32 38 91
TCGA-49-6767 LUAD 40 317 46
TCGA-4Z-AA7M BLCA 26 440 20
TCGA-4Z-AA7N BLCA 1 1 0
TCGA-4Z-AA7O BLCA 13 143 9
TCGA-4Z-AA7Q BLCA 19 143 13
TCGA-4Z-AA7R BLCA 14 290 16
TCGA-4Z-AA7S BLCA 6 54 4
TCGA-4Z-AA7W BLCA 29 377 44
TCGA-4Z-AA7Y BLCA 10 239 13
TCGA-4Z-AA80 BLCA 35 275 24
TCGA-4Z-AA81 BLCA 10 166 15
TCGA-4Z-AA82 BLCA 6 76 4
TCGA-4Z-AA83 BLCA 3 69 3
TCGA-4Z-AA84 BLCA 24 352 25
TCGA-4Z-AA86 BLCA 16 131 13
TCGA-4Z-AA87 BLCA 13 200 9
TCGA-4Z-AA89 BLCA 6 93 8
TCGA-50-5044 LUAD 18 35 26
TCGA-50-5045 LUAD 31 164 45
TCGA-50-5049 LUAD 100 409 123
TCGA-50-5051 LUAD 9 65 23
TCGA-50-5055 LUAD 4 2 0
TCGA-50-5066 LUAD 27 166 30
TCGA-50-5072 LUAD 12 110 22
TCGA-50-5930 LUAD 143 819 89
TCGA-50-5931 LUAD 20 242 23
TCGA-50-5932 LUAD 8 59 9
TCGA-50-5933 LUAD 64 334 42
TCGA-50-5935 LUAD 6 31 2
TCGA-50-5936 LUAD 6 89 9
TCGA-50-5941 LUAD 43 214 18
TCGA-50-5942 LUAD 2 21 9
TCGA-50-5944 LUAD 7 44 2
TCGA-50-5946 LUAD 59 484 41
TCGA-50-6590 LUAD 71 389 257
TCGA-50-6591 LUAD 7 38 6
TCGA-50-6592 LUAD 29 185 25
TCGA-50-6593 LUAD 21 195 41
TCGA-50-6594 LUAD 39 432 38
TCGA-50-6595 LUAD 4 42 6
TCGA-50-6597 LUAD 5 36 4
TCGA-50-6673 LUAD 31 24 21
TCGA-50-7109 LUAD 21 172 30
TCGA-50-8457 LUAD 3 41 4
TCGA-50-8459 LUAD 9 53 7
TCGA-50-8460 LUAD 2 25 3
TCGA-51-4080 LUSC 15 228 22
TCGA-53-7624 LUAD 56 647 62
TCGA-53-7626 LUAD 26 89 212
TCGA-53-7813 LUAD 20 116 11
TCGA-53-A4EZ LUAD 35 397 37
TCGA-55-1592 LUAD 70 344 73
TCGA-55-1594 LUAD 11 118 38
TCGA-55-1595 LUAD 16 124 142
TCGA-55-1596 LUAD 26 125 38
TCGA-55-5899 LUAD 35 349 24
TCGA-55-6543 LUAD 2 15 5
TCGA-55-6642 LUAD 17 48 53
TCGA-55-6712 LUAD 16 42 37
TCGA-55-6968 LUAD 35 197 157
TCGA-55-6969 LUAD 49 97 213
TCGA-55-6970 LUAD 27 91 61
TCGA-55-6971 LUAD 35 15 52
TCGA-55-6975 LUAD 15 45 24
TCGA-55-6978 LUAD 40 7 10
TCGA-55-6979 LUAD 23 26 62
TCGA-55-6980 LUAD 20 3 3
TCGA-55-6981 LUAD 19 14 26
TCGA-55-6982 LUAD 29 55 63
TCGA-55-6983 LUAD 17 48 26
TCGA-55-6984 LUAD 7 9 11
TCGA-55-6985 LUAD 59 277 87
TCGA-55-6986 LUAD 3 8 4
TCGA-55-7227 LUAD 11 126 15
TCGA-55-7281 LUAD 36 241 145
TCGA-55-7283 LUAD 14 72 87
TCGA-55-7284 LUAD 6 30 4
TCGA-55-7570 LUAD 35 309 25
TCGA-55-7573 LUAD 8 38 1
TCGA-55-7574 LUAD 18 64 43
TCGA-55-7576 LUAD 49 257 35
TCGA-55-7724 LUAD 16 73 14
TCGA-55-7725 LUAD 12 106 3
TCGA-55-7726 LUAD 13 80 8
TCGA-55-7727 LUAD 22 154 21
TCGA-55-7728 LUAD 9 69 5
TCGA-55-7815 LUAD 11 90 11
TCGA-55-7903 LUAD 13 99 15
TCGA-55-7907 LUAD 84 915 85
TCGA-55-7910 LUAD 19 255 17
TCGA-55-7911 LUAD 19 159 12
TCGA-55-7913 LUAD 22 235 24
TCGA-55-7914 LUAD 10 132 17
TCGA-55-7994 LUAD 96 1201 99
TCGA-55-7995 LUAD 30 531 39
TCGA-55-8085 LUAD 15 200 18
TCGA-55-8087 LUAD 3 20 1
TCGA-55-8089 LUAD 95 813 76
TCGA-55-8090 LUAD 3 69 4
TCGA-55-8091 LUAD 3 18 1
TCGA-55-8092 LUAD 34 382 37
TCGA-55-8094 LUAD 31 356 26
TCGA-55-8096 LUAD 8 72 9
TCGA-55-8097 LUAD 7 76 8
TCGA-55-8204 LUAD 12 144 18
TCGA-55-8205 LUAD 41 311 48
TCGA-55-8206 LUAD 0 21 3
TCGA-55-8207 LUAD 21 237 20
TCGA-55-8208 LUAD 18 76 22
TCGA-55-8301 LUAD 17 153 24
TCGA-55-8302 LUAD 56 427 48
TCGA-55-8506 LUAD 139 1330 105
TCGA-55-8507 LUAD 73 741 82
TCGA-55-8508 LUAD 8 135 13
TCGA-55-8510 LUAD 26 211 20
TCGA-55-8511 LUAD 45 396 36
TCGA-55-8512 LUAD 5 28 3
TCGA-55-8514 LUAD 17 220 17
TCGA-55-8614 LUAD 7 174 5
TCGA-55-8615 LUAD 7 82 5
TCGA-55-8616 LUAD 35 354 30
TCGA-55-8619 LUAD 4 0 1
TCGA-55-8620 LUAD 28 389 30
TCGA-55-8621 LUAD 2 4 3
TCGA-55-A48X LUAD 36 227 39
TCGA-55-A48Y LUAD 23 223 24
TCGA-55-A48Z LUAD 5 31 0
TCGA-55-A490 LUAD 99 1033 112
TCGA-55-A491 LUAD 29 268 37
TCGA-55-A492 LUAD 21 203 18
TCGA-55-A493 LUAD 22 129 23
TCGA-55-A494 LUAD 20 184 14
TCGA-55-A4DF LUAD 40 528 47
TCGA-55-A4DG LUAD 67 494 67
TCGA-56-1622 LUSC 31 143 38
TCGA-56-5897 LUSC 10 54 9
TCGA-56-5898 LUSC 11 110 14
TCGA-56-6545 LUSC 21 208 23
TCGA-56-6546 LUSC 32 250 34
TCGA-5C-A9VH LIHC 7 79 9
TCGA-5C-AAPD LIHC 6 57 6
TCGA-5N-A9KI BLCA 9 130 12
TCGA-5N-A9KM BLCA 10 177 5
TCGA-5R-AA1D LIHC 2 8 0
TCGA-60-2698 LUSC 42 625 100
TCGA-60-2707 LUSC 6 49 14
TCGA-60-2708 LUSC 19 113 55
TCGA-60-2709 LUSC 16 74 10
TCGA-60-2710 LUSC 9 162 18
TCGA-60-2711 LUSC 7 55 38
TCGA-60-2712 LUSC 14 58 17
TCGA-60-2713 LUSC 17 179 18
TCGA-60-2715 LUSC 33 10 34
TCGA-60-2722 LUSC 31 228 39
TCGA-60-2725 LUSC 4 25 79
TCGA-62-8394 LUAD 7 58 2
TCGA-62-8395 LUAD 6 49 4
TCGA-62-8397 LUAD 5 21 3
TCGA-62-8398 LUAD 5 65 5
TCGA-62-8399 LUAD 26 399 34
TCGA-62-8402 LUAD 1 31 1
TCGA-62-A46P LUAD 23 218 19
TCGA-62-A46R LUAD 10 132 12
TCGA-62-A46S LUAD 4 86 6
TCGA-62-A46U LUAD 2 28 4
TCGA-62-A46V LUAD 4 49 1
TCGA-62-A46Y LUAD 5 28 0
TCGA-63-5128 LUSC 13 249 24
TCGA-63-5131 LUSC 14 235 20
TCGA-63-6202 LUSC 28 252 24
TCGA-64-1676 LUAD 40 447 63
TCGA-64-1679 LUAD 53 365 30
TCGA-64-1681 LUAD 3 35 5
TCGA-64-5774 LUAD 15 103 17
TCGA-64-5775 LUAD 38 369 44
TCGA-64-5778 LUAD 30 357 47
TCGA-64-5779 LUAD 35 268 35
TCGA-64-5815 LUAD 15 124 13
TCGA-66-2727 LUSC 81 72 99
TCGA-66-2734 LUSC 10 50 130
TCGA-66-2744 LUSC 46 83 93
TCGA-66-2754 LUSC 62 130 115
TCGA-66-2755 LUSC 21 138 26
TCGA-66-2756 LUSC 51 357 75
TCGA-66-2757 LUSC 13 185 15
TCGA-66-2758 LUSC 54 220 46
TCGA-66-2759 LUSC 32 298 53
TCGA-66-2765 LUSC 8 66 12
TCGA-66-2766 LUSC 24 274 45
TCGA-66-2770 LUSC 13 179 16
TCGA-66-2771 LUSC 46 67 135
TCGA-66-2773 LUSC 27 289 45
TCGA-66-2778 LUSC 8 84 15
TCGA-66-2780 LUSC 10 95 18
TCGA-66-2782 LUSC 30 237 39
TCGA-66-2785 LUSC 54 750 62
TCGA-66-2786 LUSC 11 150 14
TCGA-66-2787 LUSC 55 162 233
TCGA-66-2788 LUSC 31 107 70
TCGA-66-2789 LUSC 59 173 115
TCGA-66-2791 LUSC 61 142 108
TCGA-66-2794 LUSC 6 123 10
TCGA-66-2800 LUSC 13 129 17
TCGA-67-3770 LUAD 19 149 31
TCGA-67-3771 LUAD 183 689 179
TCGA-67-3772 LUAD 12 28 9
TCGA-67-3774 LUAD 6 80 8
TCGA-67-4679 LUAD 24 224 20
TCGA-67-6215 LUAD 5 74 5
TCGA-67-6216 LUAD 4 12 4
TCGA-67-6217 LUAD 19 117 14
TCGA-69-7761 LUAD 1 18 5
TCGA-69-7764 LUAD 7 63 7
TCGA-69-7765 LUAD 50 402 49
TCGA-69-7973 LUAD 12 204 20
TCGA-69-7974 LUAD 38 359 46
TCGA-69-7978 LUAD 44 308 32
TCGA-69-7979 LUAD 108 1068 125
TCGA-69-7980 LUAD 58 572 64
TCGA-69-8253 LUAD 12 113 7
TCGA-69-8254 LUAD 8 68 3
TCGA-69-8255 LUAD 27 210 29
TCGA-69-A59K LUAD 23 378 28
TCGA-70-6722 LUSC 26 206 31
TCGA-70-6723 LUSC 4 86 9
TCGA-71-8520 LUAD 10 67 4
TCGA-73-4658 LUAD 25 127 33
TCGA-73-4659 LUAD 13 136 31
TCGA-73-4662 LUAD 14 154 20
TCGA-73-4666 LUAD 33 238 68
TCGA-73-4668 LUAD 38 343 97
TCGA-73-4670 LUAD 27 264 39
TCGA-73-4675 LUAD 4 47 8
TCGA-73-4676 LUAD 7 65 14
TCGA-73-7499 LUAD 10 41 6
TCGA-75-5122 LUAD 5 66 5
TCGA-75-5125 LUAD 18 108 20
TCGA-75-5126 LUAD 90 342 60
TCGA-75-5146 LUAD 6 157 9
TCGA-75-5147 LUAD 5 32 0
TCGA-75-6203 LUAD 2 7 1
TCGA-75-6205 LUAD 3 16 3
TCGA-75-6206 LUAD 8 72 7
TCGA-75-6207 LUAD 1 52 4
TCGA-75-6211 LUAD 44 280 25
TCGA-75-6212 LUAD 2 17 0
TCGA-75-6214 LUAD 34 505 48
TCGA-75-7025 LUAD 3 19 2
TCGA-75-7030 LUAD 2 2 1
TCGA-75-7031 LUAD 17 164 9
TCGA-78-7145 LUAD 6 87 76
TCGA-78-7146 LUAD 21 154 151
TCGA-78-7147 LUAD 33 257 16
TCGA-78-7148 LUAD 22 116 59
TCGA-78-7149 LUAD 8 96 7
TCGA-78-7150 LUAD 31 289 53
TCGA-78-7152 LUAD 16 129 9
TCGA-78-7153 LUAD 10 65 8
TCGA-78-7154 LUAD 14 140 37
TCGA-78-7155 LUAD 94 1100 258
TCGA-78-7156 LUAD 17 186 36
TCGA-78-7158 LUAD 15 108 87
TCGA-78-7159 LUAD 35 127 128
TCGA-78-7160 LUAD 9 15 6
TCGA-78-7161 LUAD 15 97 54
TCGA-78-7162 LUAD 15 36 3
TCGA-78-7163 LUAD 12 5 9
TCGA-78-7166 LUAD 16 175 9
TCGA-78-7167 LUAD 7 73 25
TCGA-78-7220 LUAD 57 650 52
TCGA-78-7535 LUAD 14 128 8
TCGA-78-7536 LUAD 44 274 231
TCGA-78-7537 LUAD 8 120 4
TCGA-78-7539 LUAD 36 314 53
TCGA-78-7540 LUAD 19 8 17
TCGA-78-7542 LUAD 36 262 33
TCGA-78-8640 LUAD 46 539 35
TCGA-78-8655 LUAD 10 84 7
TCGA-78-8660 LUAD 19 162 16
TCGA-78-8662 LUAD 69 892 68
TCGA-80-5607 LUAD 5 100 5
TCGA-80-5608 LUAD 10 45 90
TCGA-80-5611 LUAD 17 144 19
TCGA-83-5908 LUAD 17 157 20
TCGA-85-6175 LUSC 4 17 8
TCGA-85-6560 LUSC 22 292 79
TCGA-85-6561 LUSC 23 61 139
TCGA-86-6562 LUAD 4 28 6
TCGA-86-6851 LUAD 59 370 367
TCGA-86-7701 LUAD 39 77 78
TCGA-86-7711 LUAD 31 156 18
TCGA-86-7713 LUAD 11 89 48
TCGA-86-7714 LUAD 3 58 8
TCGA-86-7953 LUAD 2 34 4
TCGA-86-7954 LUAD 21 104 14
TCGA-86-7955 LUAD 19 238 25
TCGA-86-8054 LUAD 18 172 18
TCGA-86-8056 LUAD 15 201 13
TCGA-86-8073 LUAD 136 967 133
TCGA-86-8074 LUAD 3 52 6
TCGA-86-8075 LUAD 4 34 5
TCGA-86-8076 LUAD 5 38 4
TCGA-86-8278 LUAD 12 44 4
TCGA-86-8279 LUAD 37 394 31
TCGA-86-8280 LUAD 2 25 6
TCGA-86-8281 LUAD 12 180 23
TCGA-86-8358 LUAD 88 857 57
TCGA-86-8359 LUAD 14 118 12
TCGA-86-8585 LUAD 41 421 33
TCGA-86-8671 LUAD 4 5 2
TCGA-86-8672 LUAD 27 193 25
TCGA-86-8673 LUAD 33 348 42
TCGA-86-A456 LUAD 31 233 25
TCGA-86-A4JF LUAD 124 884 97
TCGA-86-A4P7 LUAD 6 25 6
TCGA-91-6829 LUAD 57 454 55
TCGA-91-6830 LUAD 23 62 61
TCGA-91-6831 LUAD 15 210 25
TCGA-91-6835 LUAD 10 26 6
TCGA-91-6836 LUAD 42 196 196
TCGA-91-6840 LUAD 23 65 33
TCGA-91-6847 LUAD 20 28 15
TCGA-91-6848 LUAD 47 225 245
TCGA-91-7771 LUAD 16 105 12
TCGA-91-8496 LUAD 5 16 0
TCGA-91-8497 LUAD 3 25 2
TCGA-91-8499 LUAD 19 251 21
TCGA-91-A4BC LUAD 27 286 38
TCGA-91-A4BD LUAD 1 15 0
TCGA-93-7347 LUAD 12 70 3
TCGA-93-7348 LUAD 8 60 8
TCGA-93-8067 LUAD 6 11 398
TCGA-93-A4JN LUAD 8 49 3
TCGA-93-A4JO LUAD 7 15 4
TCGA-93-A4JP LUAD 12 1 17
TCGA-93-A4JQ LUAD 5 31 6
TCGA-95-7039 LUAD 134 938 120
TCGA-95-7043 LUAD 58 720 259
TCGA-95-7562 LUAD 36 339 26
TCGA-95-7567 LUAD 85 646 49
TCGA-95-7944 LUAD 12 180 8
TCGA-95-7947 LUAD 28 419 36
TCGA-95-7948 LUAD 7 109 8
TCGA-95-8494 LUAD 4 72 7
TCGA-95-A4VK LUAD 25 190 20
TCGA-95-A4VN LUAD 39 250 27
TCGA-95-A4VP LUAD 6 83 7
TCGA-97-7547 LUAD 19 122 11
TCGA-97-7554 LUAD 38 316 43
TCGA-97-7937 LUAD 30 360 46
TCGA-97-7938 LUAD 25 306 34
TCGA-97-7941 LUAD 5 55 9
TCGA-97-8171 LUAD 5 43 1
TCGA-97-8172 LUAD 22 202 22
TCGA-97-8174 LUAD 11 114 14
TCGA-97-8175 LUAD 5 20 2
TCGA-97-8176 LUAD 10 108 11
TCGA-97-8177 LUAD 3 15 1
TCGA-97-8179 LUAD 11 138 8
TCGA-97-8547 LUAD 2 43 4
TCGA-97-8552 LUAD 0 16 5
TCGA-97-A4LX LUAD 11 73 7
TCGA-97-A4M0 LUAD 14 321 18
TCGA-97-A4M1 LUAD 6 22 4
TCGA-97-A4M2 LUAD 1 3 0
TCGA-97-A4M3 LUAD 18 164 12
TCGA-97-A4M5 LUAD 10 74 15
TCGA-97-A4M6 LUAD 4 23 1
TCGA-97-A4M7 LUAD 25 199 27
TCGA-99-7458 LUAD 45 340 47
TCGA-99-8025 LUAD 39 352 32
TCGA-99-8028 LUAD 26 105 21
TCGA-99-8032 LUAD 37 275 29
TCGA-99-8033 LUAD 14 120 19
TCGA-A3-3308 KIRC 8 55 11
TCGA-A3-3313 KIRC 18 35 41
TCGA-A3-3316 KIRC 71 21 12
TCGA-A3-3320 KIRC 12 52 12
TCGA-A3-3346 KIRC 54 67 9
TCGA-A3-3363 KIRC 123 37 2
TCGA-A3-3365 KIRC 19 17 16
TCGA-A3-3367 KIRC 4 49 9
TCGA-A3-3374 KIRC 70 6 3
TCGA-A5-A0G9 UCEC 49 239 15
TCGA-A5-A0GB UCEC 103 613 22
TCGA-A5-A0R7 UCEC 5 34 4
TCGA-A5-A0RA UCEC 4 69 3
TCGA-A6-5661 COAD 224 984 95
TCGA-A6-5665 COAD 715 1181 504
TCGA-A6-6653 COAD 117 931 100
TCGA-A6-6780 COAD 82 599 494
TCGA-A6-6781 COAD 70 571 1269
TCGA-A6-6782 COAD 108 81 24
TCGA-AA-3492 COAD 346 1591 338
TCGA-AD-6889 COAD 240 1379 248
TCGA-AD-6895 COAD 245 1281 177
TCGA-AD-6965 COAD 29 91 8
TCGA-AK-3427 KIRC 9 8 1
TCGA-AK-3440 KIRC 1 2 13
TCGA-AK-3444 KIRC 2 19 57
TCGA-AP-A05A UCEC 9 60 2
TCGA-AP-A0LE UCEC 86 471 15
TCGA-AP-A0LT UCEC 119 582 18
TCGA-AU-6004 COAD 183 785 77
TCGA-AX-A06H UCEC 75 346 21
TCGA-AY-6197 COAD 310 784 144
TCGA-AZ-4315 COAD 497 5136 1028
TCGA-AZ-6598 COAD 917 1855 299
TCGA-AZ-6601 COAD 84 680 1031
TCGA-B0-4827 KIRC 0 3 65
TCGA-B0-5095 KIRC 5 61 4
TCGA-B0-5099 KIRC 4 55 7
TCGA-B0-5106 KIRC 10 60 8
TCGA-B0-5119 KIRC 7 70 6
TCGA-B5-A0JR UCEC 68 512 19
TCGA-B5-A0JZ UCEC 102 443 10
TCGA-B5-A0K9 UCEC 110 652 31
TCGA-B5-A11F UCEC 4 34 1
TCGA-B5-A11S UCEC 1 43 3
TCGA-B5-A11V UCEC 1 52 2
TCGA-B7-A5TI STAD 54 504 10
TCGA-B8-5164 KIRC 6 60 14
TCGA-BA-A6DA HNSC 40 540 49
TCGA-BC-A10Y LIHC 3 47 3
TCGA-BC-A3KF LIHC 6 61 10
TCGA-BD-A2L6 LIHC 4 65 4
TCGA-BF-A1PV SKCM 19 184 57
TCGA-BF-A3DJ SKCM 7 106 9
TCGA-BF-A3DL SKCM 25 335 28
TCGA-BF-A3DM SKCM 27 332 40
TCGA-BF-A3DN SKCM 5 62 3
TCGA-BF-A5EO SKCM 24 463 45
TCGA-BF-A5EP SKCM 18 116 21
TCGA-BF-A5EQ SKCM 40 430 47
TCGA-BF-A5ER SKCM 9 146 8
TCGA-BF-A5ES SKCM 47 364 41
TCGA-BG-A0LX UCEC 56 402 12
TCGA-BG-A0M4 UCEC 90 397 37
TCGA-BG-A0MU UCEC 1 49 2
TCGA-BG-A0W1 UCEC 3 60 1
TCGA-BG-A0YV UCEC 4 67 1
TCGA-BG-A187 UCEC 3 75 3
TCGA-BL-A13I BLCA 18 71 18
TCGA-BL-A13J BLCA 17 67 18
TCGA-BL-A3JM BLCA 13 161 8
TCGA-BL-A5ZZ BLCA 5 56 81
TCGA-BP-4964 KIRC 5 46 10
TCGA-BP-4985 KIRC 8 54 7
TCGA-BP-5195 KIRC 1 53 3
TCGA-BP-5198 KIRC 1 59 3
TCGA-BP-5199 KIRC 5 59 8
TCGA-BS-A0TA UCEC 76 361 35
TCGA-BS-A0TI UCEC 4 72 6
TCGA-BS-A0TJ UCEC 92 590 20
TCGA-BS-A0V6 UCEC 1 42 4
TCGA-BT-A0S7 BLCA 3 28 5
TCGA-BT-A0YX BLCA 19 536 23
TCGA-BT-A20J BLCA 27 334 36
TCGA-BT-A20N BLCA 30 150 19
TCGA-BT-A20O BLCA 16 59 20
TCGA-BT-A20P BLCA 6 73 9
TCGA-BT-A20Q BLCA 2 84 5
TCGA-BT-A20R BLCA 13 187 13
TCGA-BT-A20T BLCA 17 211 11
TCGA-BT-A20U BLCA 5 64 3
TCGA-BT-A20V BLCA 10 80 2
TCGA-BT-A20W BLCA 12 26 5
TCGA-BT-A20X BLCA 5 48 13
TCGA-BT-A2LA BLCA 10 138 27
TCGA-BT-A2LB BLCA 23 390 104
TCGA-BT-A3PJ BLCA 23 394 24
TCGA-BT-A3PK BLCA 21 175 19
TCGA-BT-A42B BLCA 3 45 1
TCGA-BT-A42E BLCA 6 145 8
TCGA-BT-A42F BLCA 15 93 10
TCGA-BW-A5NQ LIHC 6 72 9
TCGA-C4-A0EZ BLCA 7 154 11
TCGA-C4-A0F0 BLCA 8 73 7
TCGA-C4-A0F1 BLCA 3 140 7
TCGA-C4-A0F6 BLCA 6 173 7
TCGA-C5-A1MH CESC 33 179 44
TCGA-CA-6717 COAD 1713 3979 3403
TCGA-CA-6718 COAD 229 2920 145
TCGA-CC-5262 LIHC 12 100 14
TCGA-CC-5263 LIHC 11 97 7
TCGA-CC-A3MB LIHC 4 51 7
TCGA-CC-A7IE LIHC 12 131 19
TCGA-CC-A7IH LIHC 43 598 36
TCGA-CC-A8HS LIHC 3 41 2
TCGA-CC-A8HU LIHC 5 70 7
TCGA-CC-A8HV LIHC 14 112 5
TCGA-CC-A9FS LIHC 6 81 5
TCGA-CC-A9FU LIHC 1 41 2
TCGA-CF-A1HR BLCA 17 119 13
TCGA-CF-A1HS BLCA 14 123 18
TCGA-CF-A27C BLCA 6 127 3
TCGA-CF-A3MF BLCA 4 15 2
TCGA-CF-A3MG BLCA 8 109 3
TCGA-CF-A3MH BLCA 0 33 2
TCGA-CF-A3MI BLCA 5 46 5
TCGA-CF-A47S BLCA 4 15 8
TCGA-CF-A47T BLCA 3 22 0
TCGA-CF-A47V BLCA 1 61 0
TCGA-CF-A47W BLCA 0 24 1
TCGA-CF-A47X BLCA 16 271 5
TCGA-CF-A47Y BLCA 3 50 2
TCGA-CF-A5U8 BLCA 4 39 2
TCGA-CF-A5UA BLCA 3 62 1
TCGA-CF-A7I0 BLCA 4 33 1
TCGA-CF-A9FF BLCA 8 106 6
TCGA-CF-A9FH BLCA 2 32 0
TCGA-CF-A9FL BLCA 3 46 7
TCGA-CF-A9FM BLCA 0 18 2
TCGA-CJ-4902 KIRC 6 41 5
TCGA-CJ-6031 KIRC 8 46 10
TCGA-CK-5914 COAD 420 98 22
TCGA-CK-5916 COAD 77 697 662
TCGA-CM-4743 COAD 167 734 330
TCGA-CM-4752 COAD 5 86 6
TCGA-CM-6169 COAD 739 80 11
TCGA-CM-6171 COAD 129 1059 61
TCGA-CM-6674 COAD 221 663 149
TCGA-CM-6678 COAD 18 105 7
TCGA-CN-4723 HNSC 26 650 28
TCGA-CR-7388 HNSC 42 260 227
TCGA-CR-7402 HNSC 37 480 370
TCGA-CU-A0YN BLCA 12 120 13
TCGA-CU-A0YO BLCA 9 65 3
TCGA-CU-A3KJ BLCA 16 165 31
TCGA-CU-A3QU BLCA 3 81 3
TCGA-CU-A3YL BLCA 14 203 3
TCGA-CU-A5W6 BLCA 17 178 12
TCGA-CU-A72E BLCA 4 79 7
TCGA-CV-6961 HNSC 30 405 29
TCGA-CV-7242 HNSC 18 124 140
TCGA-CV-7245 HNSC 36 242 180
TCGA-CV-7248 HNSC 22 171 64
TCGA-CV-7568 HNSC 302 1490 373
TCGA-CV-A45W HNSC 55 332 47
TCGA-CV-A45Z HNSC 86 416 69
TCGA-CV-A461 HNSC 42 465 38
TCGA-CW-5580 KIRC 5 63 10
TCGA-CW-6090 KIRC 7 76 2
TCGA-CZ-4853 KIRC 6 83 6
TCGA-D1-A0ZO UCEC 71 512 36
TCGA-D1-A0ZP UCEC 6 26 1
TCGA-D1-A0ZR UCEC 4 44 2
TCGA-D1-A101 UCEC 77 237 24
TCGA-D1-A102 UCEC 1 40 2
TCGA-D1-A15Z UCEC 5 63 2
TCGA-D1-A163 UCEC 73 504 22
TCGA-D1-A16O UCEC 5 26 4
TCGA-D1-A16S UCEC 3 40 3
TCGA-D1-A174 UCEC 124 668 27
TCGA-D1-A176 UCEC 41 339 17
TCGA-D1-A17H UCEC 92 519 39
TCGA-D1-A17K UCEC 3 43 1
TCGA-D1-A17L UCEC 3 59 2
TCGA-D1-A17M UCEC 29 262 131
TCGA-D1-A17U UCEC 26 93 245
TCGA-D1-A1NU UCEC 6 67 4
TCGA-D3-A1Q3 SKCM 23 17 12
TCGA-D3-A1Q7 SKCM 8 55 18
TCGA-D3-A3BZ SKCM 7 15 9
TCGA-D3-A51G SKCM 108 852 102
TCGA-D3-A51N SKCM 4 69 4
TCGA-D3-A51R SKCM 48 521 49
TCGA-D3-A51T SKCM 88 865 83
TCGA-D3-A5GO SKCM 103 1156 91
TCGA-D3-A5GT SKCM 6 21 1
TCGA-D5-6538 COAD 76 103 7
TCGA-D5-6928 COAD 334 1264 192
TCGA-D5-6930 COAD 190 1046 82
TCGA-D6-6516 HNSC 182 1200 248
TCGA-D7-A6EY STAD 214 996 51
TCGA-D9-A3Z3 SKCM 10 96 11
TCGA-D9-A3Z4 SKCM 10 112 10
TCGA-D9-A4Z2 SKCM 2 18 0
TCGA-D9-A4Z3 SKCM 90 555 113
TCGA-D9-A4Z6 SKCM 20 219 19
TCGA-D9-A6EA SKCM 47 486 47
TCGA-D9-A6EG SKCM 7 55 9
TCGA-DA-A1HY SKCM 52 530 67
TCGA-DA-A1I2 SKCM 13 83 19
TCGA-DA-A1IC SKCM 47 479 310
TCGA-DA-A3F8 SKCM 73 815 81
TCGA-DD-A11C LIHC 16 73 6
TCGA-DD-A1ED LIHC 1 15 4
TCGA-DD-A1EE LIHC 144 279 51
TCGA-DD-A1EK LIHC 7 50 2
TCGA-DD-A39V LIHC 3 57 2
TCGA-DD-A3A3 LIHC 7 45 0
TCGA-DD-A3A5 LIHC 4 55 4
TCGA-DD-A4NA LIHC 0 27 0
TCGA-DD-A4NL LIHC 2 17 3
TCGA-DD-AA3A LIHC 4 36 0
TCGA-DD-AAC8 LIHC 32 462 20
TCGA-DD-AAC9 LIHC 2 63 1
TCGA-DD-AACC LIHC 11 55 5
TCGA-DD-AACD LIHC 10 70 6
TCGA-DD-AACE LIHC 3 64 2
TCGA-DD-AACG LIHC 7 87 4
TCGA-DD-AACJ LIHC 2 78 6
TCGA-DD-AACK LIHC 12 114 5
TCGA-DD-AACL LIHC 15 256 4
TCGA-DD-AACM LIHC 5 46 4
TCGA-DD-AACN LIHC 2 35 3
TCGA-DD-AACP LIHC 12 116 13
TCGA-DD-AACQ LIHC 20 169 13
TCGA-DD-AACU LIHC 5 86 9
TCGA-DD-AACX LIHC 8 106 5
TCGA-DD-AACZ LIHC 9 135 1
TCGA-DD-AAD0 LIHC 7 91 6
TCGA-DD-AAD1 LIHC 2 86 5
TCGA-DD-AAD5 LIHC 12 101 10
TCGA-DD-AAD8 LIHC 4 92 5
TCGA-DD-AADA LIHC 10 88 5
TCGA-DD-AADB LIHC 5 99 6
TCGA-DD-AADD LIHC 7 75 3
TCGA-DD-AADF LIHC 17 172 18
TCGA-DD-AADG LIHC 11 112 9
TCGA-DD-AADJ LIHC 5 57 3
TCGA-DD-AADK LIHC 6 43 4
TCGA-DD-AADL LIHC 14 100 14
TCGA-DD-AADN LIHC 56 55 33
TCGA-DD-AADP LIHC 5 90 2
TCGA-DD-AADR LIHC 7 77 2
TCGA-DD-AADS LIHC 5 118 7
TCGA-DD-AAE0 LIHC 5 52 1
TCGA-DD-AAE1 LIHC 5 40 3
TCGA-DD-AAE2 LIHC 6 63 6
TCGA-DD-AAE3 LIHC 12 122 8
TCGA-DD-AAE7 LIHC 8 184 10
TCGA-DD-AAE9 LIHC 10 89 4
TCGA-DD-AAED LIHC 10 55 2
TCGA-DD-AAEE LIHC 3 61 8
TCGA-DD-AAEH LIHC 2 76 2
TCGA-DD-AAEI LIHC 6 99 5
TCGA-DD-AAVR LIHC 2 53 2
TCGA-DD-AAVS LIHC 7 44 2
TCGA-DD-AAVX LIHC 11 52 7
TCGA-DD-AAVY LIHC 11 76 5
TCGA-DD-AAW3 LIHC 8 76 3
TCGA-DK-A1A5 BLCA 14 201 16
TCGA-DK-A1A7 BLCA 14 180 18
TCGA-DK-A1AC BLCA 53 1045 187
TCGA-DK-A1AD BLCA 20 185 15
TCGA-DK-A1AE BLCA 4 98 6
TCGA-DK-A1AF BLCA 2 11 5
TCGA-DK-A1AG BLCA 7 91 12
TCGA-DK-A2HX BLCA 7 57 11
TCGA-DK-A2I1 BLCA 41 85 110
TCGA-DK-A2I2 BLCA 13 20 47
TCGA-DK-A2I4 BLCA 62 465 79
TCGA-DK-A2I6 BLCA 11 179 45
TCGA-DK-A3IK BLCA 16 156 15
TCGA-DK-A3IL BLCA 8 161 8
TCGA-DK-A3IM BLCA 6 59 6
TCGA-DK-A3IN BLCA 21 307 12
TCGA-DK-A3IQ BLCA 7 118 12
TCGA-DK-A3IS BLCA 11 270 16
TCGA-DK-A3IT BLCA 22 352 21
TCGA-DK-A3IU BLCA 19 159 23
TCGA-DK-A3IV BLCA 1 61 4
TCGA-DK-A3WW BLCA 42 1002 47
TCGA-DK-A3WX BLCA 3 29 0
TCGA-DK-A3WY BLCA 2 1 1
TCGA-DK-A3X1 BLCA 28 689 35
TCGA-DK-A3X2 BLCA 6 101 3
TCGA-DK-A6AV BLCA 14 93 5
TCGA-DK-A6AW BLCA 142 3362 94
TCGA-DK-A6B0 BLCA 2 22 1
TCGA-DK-A6B1 BLCA 13 108 7
TCGA-DK-A6B2 BLCA 15 140 10
TCGA-DK-A6B5 BLCA 7 96 6
TCGA-DK-A6B6 BLCA 28 724 35
TCGA-DK-AA6L BLCA 23 337 15
TCGA-DK-AA6M BLCA 1 57 2
TCGA-DK-AA6P BLCA 9 101 14
TCGA-DK-AA6Q BLCA 6 97 8
TCGA-DK-AA6R BLCA 48 241 69
TCGA-DK-AA6S BLCA 22 454 20
TCGA-DK-AA6T BLCA 5 54 25
TCGA-DK-AA6U BLCA 19 314 37
TCGA-DK-AA6W BLCA 12 214 7
TCGA-DK-AA71 BLCA 29 551 21
TCGA-DK-AA74 BLCA 21 103 27
TCGA-DK-AA75 BLCA 26 346 31
TCGA-DK-AA76 BLCA 15 190 17
TCGA-DK-AA77 BLCA 17 297 14
TCGA-DM-A1D7 COAD 85 84 21
TCGA-DM-A1D9 COAD 161 86 20
TCGA-DM-A285 COAD 41 122 12
TCGA-DM-A28H COAD 73 54 61
TCGA-DR-A0ZM CESC 43 1005 45
TCGA-DS-A1OB CESC 15 12 457
TCGA-DS-A1OC CESC 23 1 231
TCGA-DX-A6YS SARC 279 54 8
TCGA-DX-A8BP SARC 83 457 65
TCGA-DX-AB2E SARC 94 632 95
TCGA-E5-A2PC BLCA 14 176 19
TCGA-E5-A4TZ BLCA 35 300 24
TCGA-E5-A4U1 BLCA 22 429 26
TCGA-E7-A3X6 BLCA 7 100 6
TCGA-E7-A3Y1 BLCA 8 105 12
TCGA-E7-A4IJ BLCA 33 242 17
TCGA-E7-A4XJ BLCA 2 34 1
TCGA-E7-A519 BLCA 4 63 2
TCGA-E7-A541 BLCA 31 199 26
TCGA-E7-A5KE BLCA 10 154 6
TCGA-E7-A5KF BLCA 8 162 5
TCGA-E7-A677 BLCA 18 180 13
TCGA-E7-A678 BLCA 1 44 1
TCGA-E7-A6MD BLCA 20 356 13
TCGA-E7-A6ME BLCA 11 100 10
TCGA-E7-A6MF BLCA 1 36 1
TCGA-E7-A7DU BLCA 11 223 10
TCGA-E7-A7DV BLCA 44 161 94
TCGA-E7-A7PW BLCA 7 58 1
TCGA-E7-A7XN BLCA 47 695 61
TCGA-E7-A85H BLCA 26 313 31
TCGA-E7-A97P BLCA 8 168 12
TCGA-E7-A97Q BLCA 4 59 2
TCGA-EB-A3HV SKCM 2 29 3
TCGA-EB-A3XB SKCM 26 360 45
TCGA-EB-A3XC SKCM 34 274 37
TCGA-EB-A3XD SKCM 22 95 22
TCGA-EB-A3XE SKCM 2 15 3
TCGA-EB-A3XF SKCM 21 299 20
TCGA-EB-A3Y7 SKCM 71 842 62
TCGA-EB-A41A SKCM 109 1377 109
TCGA-EB-A41B SKCM 32 295 23
TCGA-EB-A42Z SKCM 7 86 3
TCGA-EB-A430 SKCM 29 301 32
TCGA-EB-A431 SKCM 132 1198 139
TCGA-EB-A44N SKCM 15 97 9
TCGA-EB-A44O SKCM 43 346 56
TCGA-EB-A44P SKCM 26 237 29
TCGA-EB-A44R SKCM 3 38 2
TCGA-EB-A4IQ SKCM 2 7 0
TCGA-EB-A4IS SKCM 63 345 63
TCGA-EB-A4OY SKCM 2 43 3
TCGA-EB-A4OZ SKCM 3 5 1
TCGA-EB-A4P0 SKCM 16 138 10
TCGA-EB-A4XL SKCM 40 326 51
TCGA-EB-A551 SKCM 28 239 33
TCGA-EB-A553 SKCM 21 257 16
TCGA-EB-A5FP SKCM 21 285 34
TCGA-EB-A5SE SKCM 11 203 20
TCGA-EB-A5SF SKCM 3 24 2
TCGA-EB-A5SH SKCM 5 75 6
TCGA-EB-A5UM SKCM 34 409 46
TCGA-EB-A5VU SKCM 2 31 2
TCGA-EB-A6QZ SKCM 15 205 17
TCGA-EB-A6R0 SKCM 31 268 42
TCGA-ED-A5KG LIHC 1 3 1
TCGA-ED-A66Y LIHC 6 72 8
TCGA-ED-A8O5 LIHC 7 98 10
TCGA-ED-A8O6 LIHC 3 56 2
TCGA-EE-A20H SKCM 35 317 178
TCGA-EE-A29D SKCM 218 2585 396
TCGA-EE-A29M SKCM 107 1474 415
TCGA-EE-A29R SKCM 43 495 36
TCGA-EE-A2A2 SKCM 226 531 694
TCGA-EE-A2GC SKCM 65 1081 797
TCGA-EE-A2GJ SKCM 45 538 374
TCGA-EE-A2GP SKCM 35 443 53
TCGA-EE-A2ME SKCM 16 1 8
TCGA-EE-A2MI SKCM 50 706 166
TCGA-EE-A2MT SKCM 52 553 208
TCGA-EE-A3AF SKCM 132 679 167
TCGA-EE-A3J5 SKCM 169 1549 183
TCGA-EE-A3J7 SKCM 84 680 80
TCGA-EE-A3JA SKCM 55 745 65
TCGA-EE-A3JB SKCM 47 434 58
TCGA-EE-A3JI SKCM 113 830 118
TCGA-EI-6507 READ 120 839 42
TCGA-EI-6882 READ 236 977 152
TCGA-EI-6917 READ 379 4375 458
TCGA-EJ-7782 PRAD 38 186 96
TCGA-EP-A3JL LIHC 10 70 7
TCGA-ER-A193 SKCM 63 865 750
TCGA-ER-A194 SKCM 94 981 127
TCGA-ER-A196 SKCM 5 6 10
TCGA-ER-A197 SKCM 10 14 12
TCGA-ER-A19L SKCM 6 35 11
TCGA-ER-A19P SKCM 108 10 272
TCGA-ER-A2ND SKCM 5 81 6
TCGA-ER-A3ET SKCM 6 70 10
TCGA-ER-A3EV SKCM 0 10 52
TCGA-ER-A42H SKCM 2 49 2
TCGA-F4-6461 COAD 88 93 34
TCGA-F4-6570 COAD 96 458 1077
TCGA-F4-6809 COAD 8 33 95
TCGA-F4-6854 COAD 7 46 61
TCGA-F4-6855 COAD 4 30 56
TCGA-F4-6856 COAD 70 291 625
TCGA-F5-6814 READ 202 2110 6316
TCGA-FD-A3B3 BLCA 16 64 26
TCGA-FD-A3B4 BLCA 6 66 4
TCGA-FD-A3B5 BLCA 10 116 7
TCGA-FD-A3B6 BLCA 12 210 14
TCGA-FD-A3B7 BLCA 5 42 3
TCGA-FD-A3B8 BLCA 1 2 2
TCGA-FD-A3N5 BLCA 18 244 23
TCGA-FD-A3N6 BLCA 11 96 4
TCGA-FD-A3NA BLCA 6 140 8
TCGA-FD-A3SJ BLCA 12 183 20
TCGA-FD-A3SL BLCA 11 182 14
TCGA-FD-A3SM BLCA 12 173 4
TCGA-FD-A3SN BLCA 18 304 24
TCGA-FD-A3SO BLCA 20 287 6
TCGA-FD-A3SP BLCA 4 72 6
TCGA-FD-A3SQ BLCA 6 57 3
TCGA-FD-A3SS BLCA 24 312 17
TCGA-FD-A43N BLCA 10 126 7
TCGA-FD-A43P BLCA 14 298 23
TCGA-FD-A43U BLCA 6 32 5
TCGA-FD-A5BR BLCA 8 68 7
TCGA-FD-A5BS BLCA 2 8 2
TCGA-FD-A5BT BLCA 18 61 8
TCGA-FD-A5BU BLCA 4 59 3
TCGA-FD-A5BV BLCA 10 88 5
TCGA-FD-A5BX BLCA 15 306 4
TCGA-FD-A5BY BLCA 9 37 4
TCGA-FD-A5BZ BLCA 8 88 8
TCGA-FD-A5C0 BLCA 13 100 5
TCGA-FD-A5C1 BLCA 7 89 6
TCGA-FD-A62N BLCA 8 58 7
TCGA-FD-A62O BLCA 6 147 8
TCGA-FD-A62P BLCA 30 222 27
TCGA-FD-A62S BLCA 10 54 5
TCGA-FD-A6TA BLCA 9 216 17
TCGA-FD-A6TB BLCA 10 100 43
TCGA-FD-A6TC BLCA 37 579 231
TCGA-FD-A6TD BLCA 7 105 7
TCGA-FD-A6TE BLCA 12 148 57
TCGA-FD-A6TF BLCA 13 89 13
TCGA-FD-A6TG BLCA 36 214 34
TCGA-FD-A6TH BLCA 11 137 5
TCGA-FD-A6TI BLCA 8 100 8
TCGA-FD-A6TK BLCA 6 67 14
TCGA-FI-A2EW UCEC 5 86 5
TCGA-FJ-A3Z7 BLCA 19 269 8
TCGA-FJ-A3Z9 BLCA 3 61 1
TCGA-FJ-A3ZE BLCA 16 349 14
TCGA-FJ-A3ZF BLCA 15 201 5
TCGA-FJ-A871 BLCA 1 43 0
TCGA-FR-A2OS SKCM 4 13 0
TCGA-FR-A3YO SKCM 52 567 50
TCGA-FR-A726 SKCM 477 4831 625
TCGA-FR-A728 SKCM 25 260 33
TCGA-FS-A1Z3 SKCM 70 781 58
TCGA-FS-A1ZU SKCM 15 15 21
TCGA-FS-A4FC SKCM 42 566 25
TCGA-FT-A61P BLCA 8 104 15
TCGA-FV-A2QQ LIHC 14 96 9
TCGA-FV-A3R3 LIHC 7 36 4
TCGA-FW-A5DX SKCM 22 126 22
TCGA-G2-A2EC BLCA 11 141 16
TCGA-G2-A2EF BLCA 21 201 20
TCGA-G2-A2EJ BLCA 13 151 124
TCGA-G2-A2EK BLCA 2 57 4
TCGA-G2-A2EL BLCA 7 195 7
TCGA-G2-A2EO BLCA 37 390 317
TCGA-G2-A2ES BLCA 15 221 174
TCGA-G2-A3IB BLCA 4 82 0
TCGA-G2-A3IE BLCA 15 294 9
TCGA-G2-AA3B BLCA 43 496 42
TCGA-G2-AA3D BLCA 16 89 12
TCGA-G2-AA3F BLCA 11 114 9
TCGA-G3-A25W LIHC 59 68 19
TCGA-G3-A25Z LIHC 40 57 10
TCGA-G3-A3CH LIHC 7 26 2
TCGA-G3-A3CI LIHC 0 11 2
TCGA-G3-A5SJ LIHC 11 82 13
TCGA-G3-AAUZ LIHC 4 68 4
TCGA-G3-AAV0 LIHC 12 138 8
TCGA-G3-AAV1 LIHC 8 42 4
TCGA-G3-AAV2 LIHC 6 39 4
TCGA-G3-AAV3 LIHC 4 76 3
TCGA-G3-AAV4 LIHC 3 85 9
TCGA-G3-AAV7 LIHC 5 65 5
TCGA-G4-6302 COAD 1128 305 123
TCGA-G4-6306 COAD 11 94 5
TCGA-G4-6309 COAD 182 625 135
TCGA-G4-6320 COAD 140 809 60
TCGA-G4-6588 COAD 140 658 1196
TCGA-G4-6626 COAD 30 62 45
TCGA-GC-A3BM BLCA 4 72 35
TCGA-GC-A3I6 BLCA 13 143 13
TCGA-GC-A3OO BLCA 7 49 4
TCGA-GC-A3RC BLCA 11 284 11
TCGA-GC-A3RD BLCA 8 63 5
TCGA-GC-A3WC BLCA 12 127 3
TCGA-GC-A3YS BLCA 7 184 8
TCGA-GC-A6I1 BLCA 10 172 9
TCGA-GC-A6I3 BLCA 15 94 60
TCGA-GD-A2C5 BLCA 12 57 168
TCGA-GD-A3OP BLCA 15 81 11
TCGA-GD-A3OQ BLCA 9 73 6
TCGA-GD-A3OS BLCA 9 79 3
TCGA-GD-A6C6 BLCA 16 217 11
TCGA-GD-A76B BLCA 9 136 12
TCGA-GF-A6C9 SKCM 229 1441 316
TCGA-GJ-A3OU LIHC 6 32 4
TCGA-GJ-A9DB LIHC 5 63 4
TCGA-GN-A264 SKCM 12 18 22
TCGA-GN-A269 SKCM 23 373 170
TCGA-GN-A26D SKCM 19 12 25
TCGA-GN-A4U5 SKCM 42 214 54
TCGA-GU-A42P BLCA 13 159 19
TCGA-GU-A42Q BLCA 6 153 4
TCGA-GU-A42R BLCA 10 119 6
TCGA-GU-A762 BLCA 11 65 20
TCGA-GU-A763 BLCA 6 48 5
TCGA-GU-A764 BLCA 16 45 9
TCGA-GU-A766 BLCA 11 142 10
TCGA-GU-A767 BLCA 27 216 28
TCGA-GU-AATO BLCA 14 230 28
TCGA-GU-AATP BLCA 13 238 21
TCGA-GV-A3JV BLCA 15 84 7
TCGA-GV-A3JW BLCA 5 60 5
TCGA-GV-A3JX BLCA 11 191 13
TCGA-GV-A3JZ BLCA 23 381 18
TCGA-GV-A3QF BLCA 7 112 6
TCGA-GV-A3QG BLCA 9 72 3
TCGA-GV-A3QH BLCA 11 139 3
TCGA-GV-A3QI BLCA 28 364 27
TCGA-GV-A3QK BLCA 9 113 7
TCGA-GV-A40E BLCA 14 78 7
TCGA-GV-A40G BLCA 8 119 9
TCGA-GV-A6ZA BLCA 20 257 12
TCGA-HF-A5NB STAD 178 1178 42
TCGA-HQ-A2OE BLCA 12 122 4
TCGA-HQ-A2OF BLCA 14 83 7
TCGA-HQ-A5ND BLCA 11 67 2
TCGA-HR-A2OH SKCM 29 28 54
TCGA-J2-8192 LUAD 7 50 7
TCGA-J2-8194 LUAD 8 125 9
TCGA-J2-A4AD LUAD 25 194 24
TCGA-J2-A4AE LUAD 4 26 2
TCGA-J2-A4AG LUAD 10 46 6
TCGA-J9-A52C PRAD 80 400 23
TCGA-K4-A3WS BLCA 22 183 19
TCGA-K4-A3WU BLCA 21 91 9
TCGA-K4-A4AB BLCA 2 79 2
TCGA-K4-A4AC BLCA 10 109 9
TCGA-K4-A5RH BLCA 14 136 17
TCGA-K4-A5RI BLCA 3 102 6
TCGA-K4-A5RJ BLCA 19 270 15
TCGA-K4-A6FZ BLCA 15 310 18
TCGA-K4-A6MB BLCA 19 266 13
TCGA-K4-A83P BLCA 16 39 21
TCGA-K4-AAQO BLCA 12 194 11
TCGA-K7-AAU7 LIHC 4 60 4
TCGA-KN-8428 KICH 83 536 39
TCGA-KQ-A41N BLCA 9 114 115
TCGA-KQ-A41O BLCA 14 198 7
TCGA-KQ-A41P BLCA 10 241 17
TCGA-KQ-A41Q BLCA 30 90 40
TCGA-KQ-A41R BLCA 23 567 34
TCGA-KR-A7K0 LIHC 7 67 10
TCGA-KU-A66S HNSC 31 338 21
TCGA-L4-A4E5 LUAD 18 261 25
TCGA-L4-A4E6 LUAD 0 1 2
TCGA-L5-A43J ESCA 84 650 18
TCGA-L5-A8NM ESCA 267 1204 95
TCGA-L9-A443 LUAD 20 193 26
TCGA-L9-A444 LUAD 52 361 63
TCGA-LC-A66R BLCA 11 101 4
TCGA-LT-A5Z6 BLCA 23 296 28
TCGA-MN-A4N1 LUAD 38 328 31
TCGA-MN-A4N5 LUAD 39 332 36
TCGA-MP-A4SV LUAD 21 168 19
TCGA-MP-A4SW LUAD 6 36 4
TCGA-MP-A4SY LUAD 12 86 12
TCGA-MP-A4T2 LUAD 3 42 7
TCGA-MP-A4T4 LUAD 47 215 30
TCGA-MP-A4T6 LUAD 4 45 3
TCGA-MP-A4T7 LUAD 14 108 5
TCGA-MP-A4T8 LUAD 9 89 13
TCGA-MP-A4T9 LUAD 3 9 0
TCGA-MP-A4TA LUAD 27 224 35
TCGA-MP-A4TC LUAD 10 198 16
TCGA-MP-A4TD LUAD 9 46 9
TCGA-MP-A4TE LUAD 10 111 3
TCGA-MP-A4TF LUAD 29 285 34
TCGA-MP-A4TI LUAD 25 90 12
TCGA-MP-A4TK LUAD 31 229 18
TCGA-MP-A5C7 LUAD 3 53 3
TCGA-MR-A520 LIHC 1 12 1
TCGA-MR-A8JO LIHC 3 17 2
TCGA-MV-A51V BLCA 112 896 109
TCGA-MX-A5UJ STAD 208 1139 52
TCGA-ND-A4WC UCS 197 3175 332
TCGA-NI-A8LF LIHC 5 82 3
TCGA-NJ-A4YF LUAD 36 421 86
TCGA-NJ-A4YG LUAD 17 72 8
TCGA-NJ-A4YI LUAD 36 346 38
TCGA-NJ-A4YP LUAD 29 365 22
TCGA-NJ-A55A LUAD 5 30 1
TCGA-NJ-A55O LUAD 9 68 6
TCGA-NJ-A55R LUAD 14 188 18
TCGA-O1-A52J LUAD 12 127 12
TCGA-PK-A5HB ACC 101 871 66
TCGA-PQ-A6FI BLCA 5 129 7
TCGA-PQ-A6FN BLCA 8 61 3
TCGA-QQ-A8VF SARC 73 669 30
TCGA-R3-A69X BLCA 8 139 19
TCGA-R5-A7ZI STAD 132 653 46
TCGA-RC-A6M3 LIHC 7 62 7
TCGA-RG-A7D4 LIHC 11 60 10
TCGA-RP-A693 SKCM 76 535 111
TCGA-RP-A694 SKCM 45 513 60
TCGA-RP-A695 SKCM 54 634 74
TCGA-S5-A6DX BLCA 20 545 31
TCGA-S5-AA26 BLCA 13 193 6
TCGA-SW-A7EA STAD 56 516 26
TCGA-SY-A9G0 BLCA 3 23 2
TCGA-SY-A9G5 BLCA 51 807 46
TCGA-T1-A6J8 LIHC 11 69 4
TCGA-TN-A7HL HNSC 24 469 40
TCGA-UB-A7MB LIHC 80 591 692
TCGA-UB-A7MD LIHC 7 89 9
TCGA-UB-AA0U LIHC 5 58 7
TCGA-UB-AA0V LIHC 3 23 3
TCGA-UY-A78K BLCA 65 390 60
TCGA-UY-A78L BLCA 12 128 27
TCGA-UY-A78M BLCA 8 113 7
TCGA-UY-A78N BLCA 17 161 53
TCGA-UY-A78O BLCA 7 138 12
TCGA-UY-A8OB BLCA 21 274 20
TCGA-UY-A9PA BLCA 12 47 5
TCGA-UY-A9PB BLCA 38 375 24
TCGA-UY-A9PD BLCA 12 232 14
TCGA-UY-A9PE BLCA 15 167 15
TCGA-UY-A9PF BLCA 18 358 21
TCGA-UY-A9PH BLCA 13 275 20
TCGA-W5-AA39 CHOL 62 585 43
TCGA-WJ-A86L LIHC 1 111 6
TCGA-WQ-AB4B LIHC 6 46 8
TCGA-WX-AA46 LIHC 8 25 3
TCGA-WX-AA47 LIHC 5 29 2
TCGA-X6-A7WA SARC 307 44 8
TCGA-XF-A8HH BLCA 8 73 6
TCGA-XF-A8HI BLCA 4 54 1
TCGA-XF-A9SG BLCA 12 152 11
TCGA-XF-A9SH BLCA 2 29 3
TCGA-XF-A9SI BLCA 28 106 31
TCGA-XF-A9SJ BLCA 14 146 20
TCGA-XF-A9SK BLCA 5 123 4
TCGA-XF-A9SM BLCA 23 131 25
TCGA-XF-A9SP BLCA 18 203 25
TCGA-XF-A9ST BLCA 34 464 26
TCGA-XF-A9SU BLCA 5 38 1
TCGA-XF-A9SV BLCA 4 47 10
TCGA-XF-A9SW BLCA 7 37 3
TCGA-XF-A9SX BLCA 12 79 4
TCGA-XF-A9SY BLCA 27 234 25
TCGA-XF-A9SZ BLCA 16 154 22
TCGA-XF-A9T2 BLCA 5 71 3
TCGA-XF-A9T3 BLCA 21 312 24
TCGA-XF-A9T4 BLCA 3 27 5
TCGA-XF-A9T5 BLCA 32 558 28
TCGA-XF-A9T6 BLCA 18 267 17
TCGA-XF-AAME BLCA 4 5 3
TCGA-XF-AAMF BLCA 1 65 3
TCGA-XF-AAMG BLCA 49 791 40
TCGA-XF-AAMH BLCA 3 51 2
TCGA-XF-AAMJ BLCA 5 22 4
TCGA-XF-AAML BLCA 12 405 20
TCGA-XF-AAMQ BLCA 8 155 8
TCGA-XF-AAMR BLCA 8 79 8
TCGA-XF-AAMT BLCA 18 80 9
TCGA-XF-AAMW BLCA 2 23 0
TCGA-XF-AAMX BLCA 14 268 17
TCGA-XF-AAMY BLCA 7 92 6
TCGA-XF-AAMZ BLCA 29 145 20
TCGA-XF-AAN0 BLCA 15 354 12
TCGA-XF-AAN1 BLCA 8 62 2
TCGA-XF-AAN2 BLCA 10 382 11
TCGA-XF-AAN3 BLCA 11 110 4
TCGA-XF-AAN4 BLCA 4 2 1
TCGA-XF-AAN5 BLCA 20 259 15
TCGA-XF-AAN7 BLCA 9 117 11
TCGA-XK-AAIW PRAD 358 5513 464
TCGA-XR-A8TC LIHC 6 37 12
TCGA-XR-A8TD LIHC 8 45 4
TCGA-XR-A8TF LIHC 4 115 9
TCGA-XR-A8TG LIHC 5 64 2
TCGA-YA-A8S7 LIHC 4 52 5
TCGA-YB-A89D PAAD 1 0 19
TCGA-YC-A8S6 BLCA 6 56 9
TCGA-YC-A9TC BLCA 9 101 10
TCGA-YF-AA3L BLCA 14 250 15
TCGA-YF-AA3M BLCA 13 110 14
TCGA-ZB-A966 THYM 93 556 43
TCGA-ZF-A9R0 BLCA 16 166 1
TCGA-ZF-A9R3 BLCA 6 68 7
TCGA-ZF-A9R4 BLCA 10 216 8
TCGA-ZF-A9R5 BLCA 8 88 6
TCGA-ZF-A9R7 BLCA 32 579 18
TCGA-ZF-A9R9 BLCA 9 156 6
TCGA-ZF-A9RC BLCA 56 618 48
TCGA-ZF-A9RD BLCA 9 136 5
TCGA-ZF-A9RE BLCA 3 43 1
TCGA-ZF-A9RF BLCA 20 188 21
TCGA-ZF-A9RG BLCA 15 164 8
TCGA-ZF-A9RM BLCA 3 63 3
TCGA-ZF-A9RN BLCA 8 145 9
TCGA-ZF-AA4N BLCA 11 124 10
TCGA-ZF-AA4R BLCA 5 48 3
TCGA-ZF-AA4T BLCA 15 59 8
TCGA-ZF-AA4U BLCA 5 47 4
TCGA-ZF-AA4W BLCA 50 392 22
TCGA-ZF-AA51 BLCA 35 532 38
TCGA-ZF-AA53 BLCA 8 105 9
TCGA-ZF-AA54 BLCA 9 158 5
TCGA-ZF-AA56 BLCA 5 77 8
TCGA-ZF-AA58 BLCA 11 145 17
TCGA-ZF-AA5H BLCA 1 48 3
TCGA-ZF-AA5N BLCA 4 43 2
TCGA-ZF-AA5P BLCA 4 12 4
TCGA-ZP-A9CV LIHC 9 82 10
TCGA-ZP-A9CY LIHC 6 70 2
TCGA-ZP-A9CZ LIHC 5 38 1
TCGA-ZP-A9D0 LIHC 2 47 1
TCGA-ZP-A9D1 LIHC 5 104 6
TCGA-ZP-A9D2 LIHC 3 50 3
TCGA-ZS-A9CF LIHC 5 73 5
d TCGA (MC3)
Total Cerebro Total TCGA
164 176
264 267
1051 1095
98 99
154 158
214 221
128 234
693 709
443 482
118 117
236 271
514 786
168 176
169 239
221 224
234 240
29 33
38 37
38 40
169 173
368 411
37 30
28 29
47 52
129 132
420 425
305 316
29 26
106 101
159 172
5 7
165 174
25 14
62 83
48 53
13 9
216 204
101 97
54 46
231 281
447 438
277 262
183 189
9 2
54 55
967 1017
188 200
599 584
1847 1963
66 64
110 105
164 164
105 91
544 562
116 127
102 153
187 232
227 284
213 245
292 303
49 88
118 127
141 141
30 52
1087 2450
105 105
113 157
127 276
137 269
124 129
233 241
178 182
381 470
120 118
163 163
324 332
110 105
320 335
364 357
87 91
168 174
71 74
176 186
209 284
132 155
156 156
250 267
305 296
136 134
38 38
518 517
180 181
308 306
623 633
71 75
153 145
132 133
134 134
180 187
200 198
258 258
184 192
424 414
120 124
63 59
181 175
318 321
95 90
83 80
59 58
85 78
58 53
63 62
34 32
65 62
85 79
74 69
114 115
47 47
116 107
61 63
66 62
117 109
123 129
64 60
276 284
151 160
149 152
1148 1158
140 149
446 482
292 294
372 370
191 204
288 295
568 564
103 142
89 82
127 128
196 203
121 125
228 226
242 238
179 189
99 96
183 211
363 367
238 256
271 299
638 658
11 15
80 87
213 227
94 101
642 613
406 408
41 35
20 24
3 2
292 294
121 127
112 120
69 72
126 127
97 91
120 116
82 75
408 425
187 196
178 188
116 117
116 110
211 268
134 125
190 224
544 550
271 272
95 91
164 167
180 179
569 643
233 272
343 361
14 24
157 142
51 31
24 19
291 262
122 110
61 78
613 689
338 392
798 849
27 34
182 187
256 256
29 34
64 40
4 4
169 237
19 44
161 169
119 242
272 312
84 80
122 128
259 262
110 189
457 451
350 371
394 391
721 936
191 192
99 86
518 532
528 523
188 197
155 151
40 35
60 63
32 28
309 310
99 102
114 187
86 96
161 220
427 725
122 159
190 187
71 90
197 192
223 241
25 22
157 150
29 28
96 90
144 148
30 39
26 23
258 260
191 186
461 535
85 117
63 81
70 129
357 363
466 460
2 1
156 152
162 156
304 306
60 58
406 421
249 252
310 299
176 181
82 80
72 72
376 377
147 144
213 209
99 101
53 61
195 209
509 532
74 88
6 2
193 196
122 132
962 908
262 265
67 68
398 376
37 33
95 98
257 232
23 30
51 46
543 525
460 646
45 44
214 210
216 236
471 470
46 48
41 40
55 45
193 202
44 45
62 60
27 28
243 250
703 709
115 301
136 127
432 434
414 417
129 156
140 266
151 163
384 373
17 20
65 101
58 79
232 354
146 310
118 152
50 67
60 69
47 17
49 88
23 6
33 40
84 118
65 74
16 20
336 364
11 12
137 141
277 386
86 159
36 34
344 334
46 39
82 107
306 292
89 87
118 109
93 88
176 175
78 74
101 101
112 114
999 1000
274 272
178 171
257 259
142 149
1297 1300
561 570
215 218
23 21
908 889
72 73
21 19
416 419
387 382
80 81
83 84
156 162
352 359
21 24
258 257
94 98
170 177
483 475
1469 1435
814 823
143 148
237 231
441 432
33 31
237 237
181 179
89 87
389 384
4 1
417 419
6 7
263 266
246 247
36 31
1132 1145
297 305
224 221
151 152
204 198
568 575
561 561
174 181
64 63
121 124
229 231
282 284
86 88
63 63
139 142
187 182
10 8
667 725
55 63
132 168
90 84
171 180
62 93
72 75
196 197
43 44
259 267
29 104
65 60
55 53
26 24
70 70
425 433
32 32
241 237
142 144
90 92
30 32
53 50
33 28
262 273
249 255
280 276
487 510
418 395
38 40
118 120
407 413
387 404
303 303
139 137
153 171
60 180
129 176
192 245
159 164
408 432
198 200
274 266
330 351
74 78
298 319
192 195
113 202
316 334
92 99
105 113
267 276
804 812
161 164
217 395
138 177
232 288
203 250
129 133
142 146
168 180
872 868
40 37
86 88
248 244
79 79
16 16
136 131
19 23
70 70
452 451
216 224
397 405
352 340
1176 1193
630 636
125 120
76 71
237 239
401 406
232 237
90 95
77 71
152 160
149 167
168 174
271 306
381 440
291 303
51 55
72 79
51 47
71 71
126 128
432 402
163 166
37 32
9 8
19 19
80 79
53 56
324 305
19 17
539 553
22 21
4 3
181 173
93 163
175 305
290 273
138 175
104 103
320 342
145 138
75 73
154 177
1194 1358
203 222
123 195
162 255
24 21
112 151
51 39
17 14
191 184
80 98
707 702
142 136
318 505
128 124
350 367
27 25
298 295
585 574
94 91
181 178
961 960
105 105
55 135
161 163
174 177
21 25
314 371
84 200
32 34
429 737
116 155
187 174
100 137
61 66
36 38
125 118
257 263
190 190
216 214
1103 1100
55 58
38 39
43 42
56 48
431 425
27 31
192 203
945 914
132 130
462 454
9 7
220 218
381 390
264 258
1008 981
31 31
511 509
85 123
225 235
36 32
238 392
88 98
48 43
272 470
121 117
21 16
28 27
270 272
313 324
16 15
82 73
68 68
17 409
57 52
22 19
13 18
36 37
1072 1058
778 979
375 365
731 695
192 188
447 455
116 117
76 79
215 210
289 277
89 90
141 133
354 359
390 406
331 340
60 64
48 44
224 224
125 128
25 22
118 119
18 16
149 146
45 47
16 21
84 80
335 339
28 26
4 3
182 176
84 89
27 24
224 226
385 387
391 384
131 126
312 304
134 139
63 66
53 76
92 33
64 64
121 76
160 39
36 33
53 58
76 9
288 254
716 635
39 38
73 72
1208 1079
1896 1685
1048 1031
681 1093
641 1840
189 105
1937 1929
1619 1627
1526 1458
120 99
17 9
3 15
21 76
69 62
557 486
701 600
968 862
421 367
1094 928
5633 6164
2772 2154
764 1711
3 68
66 65
59 62
70 68
77 76
580 531
545 453
762 683
38 35
44 46
53 54
558 514
66 74
580 589
50 50
67 71
69 69
203 241
113 115
360 363
359 372
67 65
487 508
134 137
470 477
155 154
411 405
458 414
487 434
50 51
63 61
71 68
78 78
89 89
84 85
174 169
61 137
51 56
62 61
54 56
60 62
64 67
437 396
76 78
682 610
43 46
31 33
555 559
361 370
180 169
75 79
79 82
86 89
200 200
228 222
69 67
90 82
38 31
53 61
148 165
413 494
417 418
196 194
48 46
151 153
108 103
78 81
161 165
81 80
143 147
179 180
212 223
5692 7382
3149 3065
112 114
108 104
55 58
143 150
641 634
44 43
75 77
126 117
87 86
42 43
136 132
137 141
133 130
19 17
117 112
33 35
51 51
19 23
25 22
62 61
24 25
287 276
53 52
43 41
65 63
37 34
114 112
34 32
49 53
18 20
47 46
54 56
518 120
774 1359
901 1064
91 92
819 91
1188 1120
884 812
123 112
676 678
302 487
517 850
132 133
74 68
181 196
84 84
217 206
195 190
83 86
435 434
142 264
278 422
193 235
1792 1863
387 379
502 485
507 503
68 73
83 78
89 89
583 548
32 27
48 46
314 261
41 42
68 65
577 526
31 30
43 43
792 695
380 356
611 558
46 44
62 61
291 393
119 338
73 71
40 29
63 73
22 24
960 954
73 73
569 570
953 948
1259 1247
27 22
179 110
1598 1456
1236 1128
1382 1448
1210 1047
106 107
122 122
20 18
645 668
239 238
533 533
62 64
582 597
96 102
526 789
888 896
89 79
16 19
423 330
57 52
60 59
52 45
59 59
27 27
19 20
40 36
494 482
65 64
66 60
80 76
67 66
94 91
80 84
126 119
271 260
51 50
37 38
128 129
189 182
91 95
114 111
144 136
98 97
88 91
113 111
96 97
98 93
104 105
82 78
189 190
123 121
62 60
49 47
114 114
111 88
95 92
84 79
123 125
57 53
45 43
69 69
134 130
192 194
99 93
65 57
64 69
78 78
105 104
55 55
51 46
63 59
87 81
84 79
215 217
194 198
1098 1232
205 200
102 104
13 16
98 103
64 68
126 195
33 67
527 544
190 224
172 171
169 169
65 65
328 319
125 130
281 286
374 373
178 182
62 65
1044 1049
32 29
3 2
717 724
107 104
107 98
3504 3456
24 23
121 115
155 150
103 102
752 759
360 352
58 59
110 115
103 105
289 310
476 474
59 79
333 351
226 221
580 572
124 130
372 377
205 207
314 311
169 105
247 106
163 134
127 115
1048 1050
27 469
24 232
333 62
540 522
726 727
190 195
335 324
451 455
107 106
113 117
275 259
36 35
67 65
230 225
164 160
170 167
198 193
45 45
376 369
111 110
37 37
234 233
205 255
65 59
742 756
339 344
176 180
63 61
31 32
386 405
308 311
117 117
17 18
320 319
913 904
1486 1486
327 318
93 89
330 333
1330 1337
112 106
389 402
263 266
41 40
9 7
408 408
45 46
8 6
154 148
366 377
267 272
278 273
306 319
214 223
27 26
80 81
443 455
33 33
220 222
299 310
4 4
78 80
105 108
59 58
352 495
2803 2981
1581 1889
538 531
757 1225
1146 1878
583 912
478 496
17 9
756 872
605 761
811 846
1718 1732
764 760
800 810
481 492
943 948
959 881
1213 1129
4754 4833
224 282
80 77
928 1615
1075 1108
11 16
24 26
41 46
118 282
86 87
76 80
10 62
51 51
181 127
554 1535
41 128
53 107
34 86
361 916
2312 8426
80 90
72 70
126 123
222 224
47 45
3 4
262 267
107 100
146 148
195 203
193 196
185 177
322 328
307 293
76 78
63 60
336 329
136 133
312 321
38 37
76 75
10 10
79 69
63 62
98 93
321 310
46 41
96 96
113 105
96 95
66 65
153 155
252 249
64 59
225 233
110 143
616 810
112 112
160 205
102 102
250 248
148 142
108 108
73 81
91 91
288 277
64 62
365 363
216 206
44 43
17 13
619 617
5308 5456
285 293
851 839
30 36
608 591
112 119
110 105
43 40
148 148
152 157
222 221
164 275
59 61
202 202
427 707
236 395
86 82
309 303
539 538
105 101
125 123
127 87
97 67
33 28
11 13
93 95
72 72
150 146
50 46
45 43
80 79
88 94
70 70
1433 428
105 99
807 760
949 869
798 1854
92 107
76 107
156 156
56 53
295 295
71 68
139 130
191 192
182 181
109 154
69 225
96 92
82 79
88 82
233 228
145 148
1670 1757
38 36
68 67
30 40
396 543
31 37
256 268
172 178
159 157
129 125
76 85
54 53
61 54
153 152
243 244
244 258
251 259
99 91
65 65
202 204
404 399
119 118
81 75
150 142
392 391
122 120
92 85
127 128
277 269
1356 1220
134 126
97 90
78 69
57 82
57 57
133 134
219 218
30 28
56 52
480 423
205 202
112 100
81 81
119 118
150 153
105 108
289 285
325 328
285 279
55 60
206 205
64 64
619 575
123 229
212 205
251 258
120 130
590 601
74 77
369 359
279 286
1 3
734 668
1471 1299
213 219
413 424
112 105
319 324
366 359
371 368
189 187
42 40
98 98
45 49
262 245
49 48
122 113
98 102
12 9
251 259
208 214
55 55
121 114
314 319
115 102
260 247
56 56
13 13
20 19
1008 1005
1347 1191
3372 3507
87 85
457 507
89 80
382 384
394 387
35 31
77 74
202 206
139 139
972 937
134 136
69 64
742 699
147 158
785 699
69 69
71 70
611 646
558 573
688 708
565 576
206 199
572 542
26 25
858 853
80 73
493 509
671 1283
96 98
63 65
26 26
455 450
140 155
121 120
178 214
145 150
295 294
59 52
413 399
244 246
182 182
376 379
288 295
647 628
112 117
52 54
33 28
34 31
351 52
81 79
58 55
164 163
31 32
134 137
160 166
128 127
154 156
221 228
498 490
43 39
51 57
44 40
91 83
261 259
170 176
76 74
333 336
30 32
590 586
285 284
9 8
66 68
840 831
54 53
27 26
417 425
163 163
87 87
98 89
25 23
282 285
99 98
174 165
369 366
70 64
392 393
121 114
6 3
279 274
126 128
5871 5977
43 49
53 49
119 124
69 66
56 57
1 19
62 65
110 111
264 265
123 124
649 599
182 167
74 75
226 224
96 94
611 597
165 162
674 666
145 141
46 44
208 209
179 172
66 66
153 154
135 134
53 51
74 67
52 51
442 414
567 570
113 114
167 163
82 85
156 162
49 51
47 45
16 16
91 92
76 72
43 39
49 48
109 110
53 53
78 78
Table S10. Concordance results for Cerebro and TCGA for driver
0
1
1
1
0
0
1
0
1
1
0
1
1
1
1
0
1
1
1
0
0
1
0
0
0
1
1
1
1
1
1
1
1
0
1
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
0
0
0
0
1
1
1
1
1
1
Table S12. Evaluation of TruSeq false positive calls using raw CS
TruSeq
SampleID Putative Mutation Classification Reported
MAF (%)
Observed
Number of WT Number of Putative Number of WT Number of Putative
Putative MAF in
Reads in CS125 Mutant Reads in Reads in Oncomine Mutant Reads in
CS125 bam file
bam file CS125 bam file bam file Oncomine bam file
(%)
0.00
0.00
0.10
0.11
0.15
0.25
0.21
0.00
0.00
0.00
0.06
0.13
0.17
0.00
0.00
0.00
0.03
0.04
0.05
0.13
0.20
0.00
0.00
0.00
0.00
0.00
0.00
0.12
0.14
0.35
0.36
2.50
0.00
0.00
0.00
0.00
0.05
0.06
0.16
0.00
0.00
0.00
0.02
0.03
0.05
0.05
0.14
0.14
0.00
0.00
0.00
0.00
0.03
0.09
0.21
0.45
0.00
0.00
0.00
0.00
0.00
0.15
0.34
0.00
0.00
0.00
0.00
0.00
0.00
0.03
0.05
0.06
0.07
0.00
0.00
0.02
0.03
0.04
0.05
0.05
0.06
0.07
0.12
0.14
0.15
0.25
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.07
0.08
0.08
0.20
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.02
0.02
0.04
0.05
0.06
0.11
0.12
0.13
0.29
0.00
0.00
0.00
0.00
0.03
0.03
0.06
0.21
0.24
0.38
0.00
0.00
0.00
0.00
0.02
0.10
0.10
0.25
0.00
0.00
0.03
0.08
0.10
0.14
0.25
0.00
0.00
0.00
0.00
0.00
0.00
0.09
0.20
35.25
32.88
37.97
62.61
23.60
61.91
18.69
27.52
28.23
35.88
45.83
69.88
28.18
30.30
69.91
Table S13. Comparison of mutation callers for clinical samples*
Performance Metric Cerebro
Point
TP FN 95% CI TP
Estimate
Point
TP FP 95% CI TP
Estimate
*SBS: Single base substitution, TP: True Positive, FN: False Negative, FP: False Positive, 95% CI: 9
MuTect2 VarDict
Point Point
FN 95% CI TP FN 95% CI
Estimate Estimate
Point Point
FP 95% CI TP FP 95% CI
Estimate Estimate
95% Confidence interval, Indel: Insertion or Deletion, PPV: Positive predictive value
Table S15. Genomic regions of interest u
Comparison