Insertion Pipeline
Bowtie2_wholegenome:
  reads:	UG19_1-HE.fastq.uq.polyn	UG19_1-HE.filter	percent
uq reads:	57975239	3239028	5.5869%
   reads: 	67212218	3800895	5.6551%
----------------
virus_structural_rna_repbase_filter:
  reads:	UG19_1-HE.filter	UG19_1-HE.nostrna	percent
uq reads:	3239028	2331467	71.9805%
   reads: 	3800895	2626070	69.0908%
----------------
TE_filter:
  reads:	UG19_1-HE.nostrna	UG19_1-HE.noTE	percent
uq reads:	2331467	2322256	99.6049%
   reads: 	2626070	2608169	99.3183%
----------------
match_dm6_mask_gen:1:
  reads:	UG19_1-HE.noGEN.front	UG19_1-HE.noGEN.front.gen	percent
uq reads:	2322256	1097874	47.2762%
   reads: 	2608169	1201285	46.0586%
----------------
match_TE:2:
  reads:	UG19_1-HE.noGEN.front	UG19_1-HE.noGEN.front.TE	percent
uq reads:	2322256	113874	4.9036%
   reads: 	2608169	128484	4.9262%
----------------
match_dm6_mask_gen:1:
  reads:	UG19_1-HE.noGEN.end	UG19_1-HE.noGEN.end.gen	percent
uq reads:	2322256	1125217	48.4536%
   reads: 	2608169	1239212	47.5127%
----------------
match_TE:2:
  reads:	UG19_1-HE.noGEN.end	UG19_1-HE.noGEN.end.TE	percent
uq reads:	2322256	112551	4.8466%
   reads: 	2608169	127167	4.8757%
----------------
Candidate insertion sites in file: UG19_1-HE_insert.txt
  reads:	19701
  uqreads:	17558
  Number of Candidate sites:	17558

Level 1 collapse of insertion sites in file: UG19_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	550

Level 1 annotation file: UG19_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
UG19_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	UG19_1-HE.noGEN.front	UG19_1-HE.noGEN.front.gendel	percent
uq reads:	2322256	1097874	47.2762%
   reads: 	2608169	1201285	46.0586%
----------------
match_dm6_mask_gen_del:1:
  reads:	UG19_1-HE.noGEN.end	UG19_1-HE.noGEN.end.gendel	percent
uq reads:	2322256	1125217	48.4536%
   reads: 	2608169	1239212	47.5127%
----------------
Candidate breakpoint sites in file: UG19_1-HE_depletion.xls
  reads:	65872
  uqreads:	58843
  Number of reads supporting candidate sites:	58843

Level 1 collapse of depletion sites in file: UG19_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3718