Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ZI220-HE.fastq.uq.polyn	ZI220-HE.filter	percent
uq reads:	43671628	2397300	5.4894%
   reads: 	45676762	2541925	5.5650%
----------------
virus_structural_rna_repbase_filter:
  reads:	ZI220-HE.filter	ZI220-HE.nostrna	percent
uq reads:	2397300	1968033	82.0937%
   reads: 	2541925	2060660	81.0669%
----------------
TE_filter:
  reads:	ZI220-HE.nostrna	ZI220-HE.noTE	percent
uq reads:	1968033	1960769	99.6309%
   reads: 	2060660	2051358	99.5486%
----------------
match_dm6_mask_gen:1:
  reads:	ZI220-HE.noGEN.front	ZI220-HE.noGEN.front.gen	percent
uq reads:	1960769	1165333	59.4324%
   reads: 	2051358	1193494	58.1807%
----------------
match_TE:2:
  reads:	ZI220-HE.noGEN.front	ZI220-HE.noGEN.front.TE	percent
uq reads:	1960769	114317	5.8302%
   reads: 	2051358	119197	5.8106%
----------------
match_dm6_mask_gen:1:
  reads:	ZI220-HE.noGEN.end	ZI220-HE.noGEN.end.gen	percent
uq reads:	1960769	1005028	51.2568%
   reads: 	2051358	1033166	50.3650%
----------------
match_TE:2:
  reads:	ZI220-HE.noGEN.end	ZI220-HE.noGEN.end.TE	percent
uq reads:	1960769	106255	5.4190%
   reads: 	2051358	111349	5.4281%
----------------
Candidate insertion sites in file: ZI220-HE_insert.txt
  reads:	32141
  uqreads:	30962
  Number of Candidate sites:	30962

Level 1 collapse of insertion sites in file: ZI220-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	543

Level 1 annotation file: ZI220-HE_level1siteannotation.xls
Insertion sites in fixed bin:
ZI220-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ZI220-HE.noGEN.front	ZI220-HE.noGEN.front.gendel	percent
uq reads:	1960769	1165333	59.4324%
   reads: 	2051358	1193494	58.1807%
----------------
match_dm6_mask_gen_del:1:
  reads:	ZI220-HE.noGEN.end	ZI220-HE.noGEN.end.gendel	percent
uq reads:	1960769	1005028	51.2568%
   reads: 	2051358	1033166	50.3650%
----------------
Candidate breakpoint sites in file: ZI220-HE_depletion.xls
  reads:	141801
  uqreads:	136404
  Number of reads supporting candidate sites:	136404

Level 1 collapse of depletion sites in file: ZI220-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	5187