Table 4. Comparison of unique and tumor specific variants in unamplified DNA, WGA DNA and RNA.

PatientID	% of uniqueunamplified withcoverage <10 inWGA bamfile	% of unique WGAwith coverage <10 inunamplified bamfile	% unique WGAin RNAwith coverage <10	WGA tumorspecific	% tumor specificconfirmed inunamplified	% WGA tumor specific inRNA (bam) withcoverage <10
118	71.7	57.6	69.9	1080	70.4	68.9
140	72.7	57.7	65.0	1644	77.9	64.2
210	84.8	21.8	62.5	630	33.3	59.4
247	90.9	5.7	–	2095	13.8	–
255	81.6	43.1	65.0	698	62.9	63.0
295	79.7	43.7	100.0	3510	81.5	100.0
278	73.3	50.9	63.4	1819	82.1	58.6
322	79.8	9.4	–	5377	11.4	–
396	79.7	53.6	64.9	1778	39.0	63.9
412	72.3	32.4	58.9	2580	60	60.5
421	78.3	27.2	100.0	994	38.1	100.0
541	82.0	25.9	–	1098	32.2	–
Average	78.9	35.8	72.2	1942	50.2	70.9
StDev	5.7	18.1	16.0	1363	19.7	16.8