Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ZS56_1-HE.fastq.uq.polyn	ZS56_1-HE.filter	percent
uq reads:	53183451	2773068	5.2142%
   reads: 	60714668	3161397	5.2070%
----------------
virus_structural_rna_repbase_filter:
  reads:	ZS56_1-HE.filter	ZS56_1-HE.nostrna	percent
uq reads:	2773068	2395186	86.3731%
   reads: 	3161397	2700718	85.4280%
----------------
TE_filter:
  reads:	ZS56_1-HE.nostrna	ZS56_1-HE.noTE	percent
uq reads:	2395186	2385065	99.5774%
   reads: 	2700718	2681793	99.2993%
----------------
match_dm6_mask_gen:1:
  reads:	ZS56_1-HE.noGEN.front	ZS56_1-HE.noGEN.front.gen	percent
uq reads:	2385065	1187092	49.7719%
   reads: 	2681793	1289124	48.0695%
----------------
match_TE:2:
  reads:	ZS56_1-HE.noGEN.front	ZS56_1-HE.noGEN.front.TE	percent
uq reads:	2385065	85452	3.5828%
   reads: 	2681793	93891	3.5011%
----------------
match_dm6_mask_gen:1:
  reads:	ZS56_1-HE.noGEN.end	ZS56_1-HE.noGEN.end.gen	percent
uq reads:	2385065	1205671	50.5509%
   reads: 	2681793	1319428	49.1995%
----------------
match_TE:2:
  reads:	ZS56_1-HE.noGEN.end	ZS56_1-HE.noGEN.end.TE	percent
uq reads:	2385065	84098	3.5260%
   reads: 	2681793	92127	3.4353%
----------------
Candidate insertion sites in file: ZS56_1-HE_insert.txt
  reads:	17439
  uqreads:	15877
  Number of Candidate sites:	15877

Level 1 collapse of insertion sites in file: ZS56_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	515

Level 1 annotation file: ZS56_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
ZS56_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ZS56_1-HE.noGEN.front	ZS56_1-HE.noGEN.front.gendel	percent
uq reads:	2385065	1187092	49.7719%
   reads: 	2681793	1289124	48.0695%
----------------
match_dm6_mask_gen_del:1:
  reads:	ZS56_1-HE.noGEN.end	ZS56_1-HE.noGEN.end.gendel	percent
uq reads:	2385065	1205671	50.5509%
   reads: 	2681793	1319428	49.1995%
----------------
Candidate breakpoint sites in file: ZS56_1-HE_depletion.xls
  reads:	62116
  uqreads:	56324
  Number of reads supporting candidate sites:	56324

Level 1 collapse of depletion sites in file: ZS56_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3430