Insertion Pipeline
Bowtie2_wholegenome:
  reads:	OSC_E.fastq.uq.polyn	OSC_E.filter	percent
uq reads:	17635270	4186534	23.7396%
   reads: 	19660695	4611817	23.4570%
----------------
virus_structural_rna_repbase_filter:
  reads:	OSC_E.filter	OSC_E.nostrna	percent
uq reads:	4186534	4175244	99.7303%
   reads: 	4611817	4591129	99.5514%
----------------
TE_filter:
  reads:	OSC_E.nostrna	OSC_E.noTE	percent
uq reads:	4175244	4172603	99.9367%
   reads: 	4591129	4588211	99.9364%
----------------
match_dm6_mask_gen:1:
  reads:	OSC_E.noGEN.front	OSC_E.noGEN.front.gen	percent
uq reads:	4172603	578750	13.8702%
   reads: 	4588211	628336	13.6946%
----------------
match_TE:2:
  reads:	OSC_E.noGEN.front	OSC_E.noGEN.front.TE	percent
uq reads:	4172603	112130	2.6873%
   reads: 	4588211	118862	2.5906%
----------------
match_dm6_mask_gen:1:
  reads:	OSC_E.noGEN.end	OSC_E.noGEN.end.gen	percent
uq reads:	4172603	243362	5.8324%
   reads: 	4588211	280604	6.1158%
----------------
match_TE:2:
  reads:	OSC_E.noGEN.end	OSC_E.noGEN.end.TE	percent
uq reads:	4172603	99846	2.3929%
   reads: 	4588211	105509	2.2996%
----------------
Candidate insertion sites in file: OSC_E_insert.txt
  reads:	14217
  uqreads:	13760
  Number of Candidate sites:	13760

Level 1 collapse of insertion sites in file: OSC_E_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	964

Level 1 annotation file: OSC_E_level1siteannotation.xls
Insertion sites in fixed bin:
OSC_E_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	OSC_E.noGEN.front	OSC_E.noGEN.front.gendel	percent
uq reads:	4172603	578750	13.8702%
   reads: 	4588211	628336	13.6946%
----------------
match_dm6_mask_gen_del:1:
  reads:	OSC_E.noGEN.end	OSC_E.noGEN.end.gendel	percent
uq reads:	4172603	243362	5.8324%
   reads: 	4588211	280604	6.1158%
----------------
Candidate breakpoint sites in file: OSC_E_depletion.xls
  reads:	17807
  uqreads:	17225
  Number of reads supporting candidate sites:	17225

Level 1 collapse of depletion sites in file: OSC_E_depletion_level1.xls
  Number of Level 1 collapsed sites:	1603