Table 2.

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

				HPV-pos.	HPV-neg.
Chr	Start	End	Q-value	loss (%)	loss (%)
2	204245506	240688770	0.0120	21.4-35.7	0-7.41
4	9729740	24650257	0.2037	21.4	0
4	40058630	47037351	0.3377	21.4	0-7.41
5	140934280	147709268	0.3785	21.4-28.6	3.7-7.41
5	60380235	66930240	0.3835	21.4	3.7-7.41
5	76699391	82660330	0.3955	21.4	7.41
17	13330532	18617236	0.4525	21.4	0-7.41
5	126804776	131251586	0.4948	21.4	0-7.41
5	72910129	75996874	0.5863	21.4	7.41
17	19272468	22200000	0.6252	21.4	0-7.41
17	7262327	9931292	0.6633	21.4	0-7.41
17	567713	3136246	0.6793	21.4	7.41
3	46788991	49028973	0.6957	28.6	7.41
17	4566909	6490288	0.7335	21.4	3.7-7.41
5	108507593	110029337	0.7552	21.4-28.6	7.41
2	241709000	242951149	0.7762	21.4	3.7-7.41
3	52397990	53145339	0.8732	21.4-35.7	7.41
5	148184554	148894433	0.8770	21.4	3.7
3	14191317	14755952	0.8862	21.4	7.41
5	140011232	140459066	0.8912	21.4	3.7-7.41
5	92966197	93334626	0.8935	21.4	7.41
5	55167345	55283138	0.9103	21.4	7.41
5	122689458	122739532	0.9113	28.6	7.41

Searching for regions with a loss of copy number in at least 20% of cases and at most 10% of controls. The two rightmost columns contain the frequency of copy nuber loss for the case and control groups, respectively