Insertion Pipeline
Bowtie2_wholegenome:
  reads:	OSC_C.fastq.uq.polyn	OSC_C.filter	percent
uq reads:	51216300	2981387	5.8212%
   reads: 	64765804	4561192	7.0426%
----------------
virus_structural_rna_repbase_filter:
  reads:	OSC_C.filter	OSC_C.nostrna	percent
uq reads:	2981387	2957388	99.1950%
   reads: 	4561192	4495720	98.5646%
----------------
TE_filter:
  reads:	OSC_C.nostrna	OSC_C.noTE	percent
uq reads:	2957388	2948569	99.7018%
   reads: 	4495720	4484633	99.7534%
----------------
match_dm6_mask_gen:1:
  reads:	OSC_C.noGEN.front	OSC_C.noGEN.front.gen	percent
uq reads:	2948569	1243459	42.1716%
   reads: 	4484633	1679739	37.4554%
----------------
match_TE:2:
  reads:	OSC_C.noGEN.front	OSC_C.noGEN.front.TE	percent
uq reads:	2948569	263552	8.9383%
   reads: 	4484633	290845	6.4854%
----------------
match_dm6_mask_gen:1:
  reads:	OSC_C.noGEN.end	OSC_C.noGEN.end.gen	percent
uq reads:	2948569	390279	13.2362%
   reads: 	4484633	836525	18.6531%
----------------
match_TE:2:
  reads:	OSC_C.noGEN.end	OSC_C.noGEN.end.TE	percent
uq reads:	2948569	133277	4.5201%
   reads: 	4484633	160993	3.5899%
----------------
Candidate insertion sites in file: OSC_C_insert.txt
  reads:	34250
  uqreads:	30604
  Number of Candidate sites:	30604

Level 1 collapse of insertion sites in file: OSC_C_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1393

Level 1 annotation file: OSC_C_level1siteannotation.xls
Insertion sites in fixed bin:
OSC_C_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	OSC_C.noGEN.front	OSC_C.noGEN.front.gendel	percent
uq reads:	2948569	1243459	42.1716%
   reads: 	4484633	1679739	37.4554%
----------------
match_dm6_mask_gen_del:1:
  reads:	OSC_C.noGEN.end	OSC_C.noGEN.end.gendel	percent
uq reads:	2948569	390279	13.2362%
   reads: 	4484633	836525	18.6531%
----------------
Candidate breakpoint sites in file: OSC_C_depletion.xls
  reads:	50369
  uqreads:	43572
  Number of reads supporting candidate sites:	43572

Level 1 collapse of depletion sites in file: OSC_C_depletion_level1.xls
  Number of Level 1 collapsed sites:	3238