Table 3.

CNVRs extracted from penile cancer data set using the query-based model with the Q_gain query

				HPV-pos.	HPV-neg.
Chr	Start	End	Q-value	gain (%)	gain (%)
9	70091642	90376569	0.2762	21.4	7.41
9	13045258	21368309	0.4562	21.4	3.7-7.41
9	119273838	124799603	0.4885	21.4-28.6	7.41
9	33871385	37132743	0.5633	21.4-28.6	3.7-7.41
20	43179131	45592378	0.6395	21.4	7.41
6	13768413	16036680	0.6512	21.4	3.7
19	50012054	52236621	0.6655	21.4	0-7.41
9	91369725	93273440	0.7047	28.6	7.41
16	463336	1664507	0.7648	21.4-28.6	3.7-7.41
17	77682387	78774742	0.7680	21.4	7.41
6	31191394	31875972	0.7963	21.4	3.7
8	37606006	38160563	0.8532	21.4	0
20	33204027	33688992	0.8565	21.4	7.41
7	54865060	55296001	0.8600	21.4	7.41
20	42433913	42557332	0.8710	21.4	7.41

Searching for regions with at least 20% of cases having a gain and at most 10% of controls having any kind of variation. The two rightmost columns contain the frequency of copy number gain for the case and control groups, respectively