Table 4.

Exome somatic calls supported by whole-genome data.

	Locus	Whole-genome						Exome
		mutation	score	Quality score		Rank			Base calls	(A:C:G:T)
				qGT	GATK	qGT	GATK	Normal	Tumor	Father	Mother
1	chr20:577556	GG > AG	61	282	99,99	1	1	0:0:90:0	27:0:64:0	1:0:104:0	1:0:90:0
2	chr18:26965596	AA > GA	87	282	99,99	1	1	77:0:1:2	63:1:20:0	106:0:0:0	84:0:0:0
3	chr9:139897201	GG > AG	59	91	66,99	16	73	0:0:23:0	6:0:18:0	0:0:24:0	0:0:21:0
4	chr2:88942555	GG > TG	93	53	-	84	-	0:0:29:0	0:0:5:3	0:0:36:0	0:0:26:0
5	chr2:88942554	AA > CA	93	52	-	86	-	30:0:0:0	0:0:6:3	0:0:36:0	0:0:26:0
6	chr7:150399212	CC > TC	93	48	60,99	98	104	0:20:0:0	1:6:0:9	0:14:0:0	0:13:0:0
7	chrX:129017457	CC > AC	41	46	45,99	109	221	0:15:0:0	5:6:0:0	0:16:0:0	0:12:0:0
8	chr16:3681082	CC > TC	89	44	30,82	118	629	0:10:0:0	0:10:0:4	0:19:0:0	0:11:0:0
9	chr10:107013067	CC > AC	30	36	-	186	-	0:52:0:0	5:57:0:1	0:74:0:0	0:72:1:0
10	chr8:72396806	TT > CT	59	24	-	398	-	0:0:0:6	0:3:0:13	0:0:0:20	0:0:0:11
11	chrX:21779651	GG > TG	89	21	36,99	483	412	2:0:13:0	0:0:7:8	0:0:9:0	0:0:14:0
12	chr5:125673987	CC > TC	97	14	6,70	790	7393	0:2:0:0	0:7:0:3	0:6:0:0	0:5:0:0
13	chr12:10156011	GG > AG	89	8	-	-	-	0:0:16:0	3:0:8:0	0:0:28:0	0:0:9:0
14	chr19:43602412	GG > AG	32	5	-	-	-	0:0:10:0	2:0:10:0	0:1:17:0	0:0:10:0
15	chr6:112619582	GG > AG	68	3	-	-	-	0:0:5:0	2:1:5:0	0:0:6:0	0:0:5:0

Somatic mutation calls of QUADGT (qGT columns) and the Genome Analysis Toolkit (GATK columns) were ranked by quality score (smaller of normal and tumor genotype call qualities in GATK's VCF output, and score of somatic call in QUADGT's VCF output that is q = - 10 log₁₀(1 - p) for a mutation with posterior probability p).

Rank is "-" at loci where no somatic mutations were inferred by QUADGT or GATK. Genome coordinates refer to NCBI 36.1/hg18 genome build.