Insertion Pipeline
Bowtie2_wholegenome:
  reads:	KN133N_1-HE.fastq.uq.polyn	KN133N_1-HE.filter	percent
uq reads:	52584048	2342588	4.4549%
   reads: 	59625314	2607309	4.3728%
----------------
virus_structural_rna_repbase_filter:
  reads:	KN133N_1-HE.filter	KN133N_1-HE.nostrna	percent
uq reads:	2342588	1976390	84.3678%
   reads: 	2607309	2198730	84.3295%
----------------
TE_filter:
  reads:	KN133N_1-HE.nostrna	KN133N_1-HE.noTE	percent
uq reads:	1976390	1966777	99.5136%
   reads: 	2198730	2185128	99.3814%
----------------
match_dm6_mask_gen:1:
  reads:	KN133N_1-HE.noGEN.front	KN133N_1-HE.noGEN.front.gen	percent
uq reads:	1966777	955058	48.5595%
   reads: 	2185128	1039207	47.5582%
----------------
match_TE:2:
  reads:	KN133N_1-HE.noGEN.front	KN133N_1-HE.noGEN.front.TE	percent
uq reads:	1966777	78112	3.9716%
   reads: 	2185128	85355	3.9062%
----------------
match_dm6_mask_gen:1:
  reads:	KN133N_1-HE.noGEN.end	KN133N_1-HE.noGEN.end.gen	percent
uq reads:	1966777	986656	50.1661%
   reads: 	2185128	1080475	49.4468%
----------------
match_TE:2:
  reads:	KN133N_1-HE.noGEN.end	KN133N_1-HE.noGEN.end.TE	percent
uq reads:	1966777	77133	3.9218%
   reads: 	2185128	84174	3.8521%
----------------
Candidate insertion sites in file: KN133N_1-HE_insert.txt
  reads:	16859
  uqreads:	15212
  Number of Candidate sites:	15212

Level 1 collapse of insertion sites in file: KN133N_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	537

Level 1 annotation file: KN133N_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
KN133N_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	KN133N_1-HE.noGEN.front	KN133N_1-HE.noGEN.front.gendel	percent
uq reads:	1966777	955058	48.5595%
   reads: 	2185128	1039207	47.5582%
----------------
match_dm6_mask_gen_del:1:
  reads:	KN133N_1-HE.noGEN.end	KN133N_1-HE.noGEN.end.gendel	percent
uq reads:	1966777	986656	50.1661%
   reads: 	2185128	1080475	49.4468%
----------------
Candidate breakpoint sites in file: KN133N_1-HE_depletion.xls
  reads:	57952
  uqreads:	52281
  Number of reads supporting candidate sites:	52281

Level 1 collapse of depletion sites in file: KN133N_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3405