Table 2.

(A) The six thresholds of GATKcan trained by randomly sampled 10 TCGA EC tumors and performances of GATKcan in the ten training experiments. (B) The four thresholds of GATKcan trained by ~10% of 539 reported indels and 112 artifacts (from 241 TCGA EC tumors), and performances of GATKcan in the ten training experiments.

Repeat	α	dNM	FS	MQ	MQRankSum	QD	Mann-Whitney test (P value)	Training
								TPR	cFPR
A. The thresholds of GATKcan for detection of single nucleotide variations
1	0.5	991.1	46.1	50.0	−7.85	0.11	0.010	98.6	10.7
2	0.5	988.1	43.6	49.5	−7.90	0.12	0.010	98.1	10.7
3	0.5	990.5	45.8	39.2	−10.10	0.05	0.010	99.3	14.3
4	0.3	985.6	49.3	48.2	−10.14	0.08	0.010	98.6	12.2
5	0.3	984.3	51.8	48.0	−10.37	0.09	0.009	98.9	11.6
6	0.4	981.5	50.9	50.0	−9.59	0.09	0.010	98.7	10.8
7	0.4	989.3	45.7	39.9	−8.97	0.05	0.082	99.3	14.0
8	0.3	982.3	55.2	50.0	−8.36	0.18	0.010	99.6	11.9
9	0.5	987.9	47.0	49.9	−10.22	0.11	0.010	98.2	10.5
10	0.5	989.1	45.6	39.9	−9.58	0.04	0.010	99.2	14.3
B. The thresholds of GATKcan for detection of indels
Repeat	α	dNM	FS	QD	Mann-Whitney test (P value)	Training
						TPR	cFPR
1	0.5	753.4	86.3	0.3	0.055	100.0	0.0
2	0.5	405.0	133.3	0.4	0.090	100.0	0.0
3	0.3	581.6	91.6	0.3	0.055	100.0	0.0
4	0.5	395.2	136.6	0.8	0.064	100.0	0.0
5	0.5	658.8	102.7	0.4	0.013	100.0	0.0
6	0.6	464.0	121.0	0.2	0.037	100.0	0.0
7	0.3	397.6	95.1	0.2	0.027	100.0	0.0
8	0.3	619.2	99.1	0.4	0.046	100.0	0.0
9	0.5	566.9	135.7	0.5	0.100	100.0	0.0
10	0.5	633.6	139.9	0.8	0.003	100.0	0.0