CTSC	chr11	-	650	E	RAB38	chr11	-	87883123	E	12	2	INTRACHR-SS-OGO-0GAP	inframe-shift

file 2 

chr11	602	63889087	HWI-ST216_106:3:67:14628:181851	-
chr11	613	69889087	HWI-ST216_106:3:24:16406:176388	+
chr11	614	80889087	HWI-ST216_106:3:21:13731:105239	+
chr11	643	94888888	HWI-ST216_111:5:22:3149:116167	+
chr11	678	98889079	HWI-ST216_106:3:5:18058:57952	+
chr11	612	108888887	HWI-ST216_106:3:8:5578:44855	+
chr5	612	63889087	HWI-ST216_106:3:67:14628:181851	-
chr3	88033200	69889087	HWI-ST216_106:3:24:16406:176388	+
chr2	88033345	80889087	HWI-ST216_106:3:21:13731:105239	+
chr1	88033376	94888888	HWI-ST216_111:5:22:3149:116167	+
chr6	88034000	98889079	HWI-ST216_106:3:5:18058:57952	+
chr7	88034123	108888887	HWI-ST216_106:3:8:5578:44855	+