Insertion Pipeline
Bowtie2_wholegenome:
  reads:	EB18_1-HE.fastq.uq.polyn	EB18_1-HE.filter	percent
uq reads:	29867316	2143508	7.1768%
   reads: 	32620577	2285684	7.0069%
----------------
virus_structural_rna_repbase_filter:
  reads:	EB18_1-HE.filter	EB18_1-HE.nostrna	percent
uq reads:	2143508	1933342	90.1952%
   reads: 	2285684	2055308	89.9209%
----------------
TE_filter:
  reads:	EB18_1-HE.nostrna	EB18_1-HE.noTE	percent
uq reads:	1933342	1929843	99.8190%
   reads: 	2055308	2048101	99.6493%
----------------
match_dm6_mask_gen:1:
  reads:	EB18_1-HE.noGEN.front	EB18_1-HE.noGEN.front.gen	percent
uq reads:	1929843	1107945	57.4111%
   reads: 	2048101	1140532	55.6873%
----------------
match_TE:2:
  reads:	EB18_1-HE.noGEN.front	EB18_1-HE.noGEN.front.TE	percent
uq reads:	1929843	145231	7.5255%
   reads: 	2048101	151777	7.4106%
----------------
match_dm6_mask_gen:1:
  reads:	EB18_1-HE.noGEN.end	EB18_1-HE.noGEN.end.gen	percent
uq reads:	1929843	950352	49.2450%
   reads: 	2048101	983357	48.0131%
----------------
match_TE:2:
  reads:	EB18_1-HE.noGEN.end	EB18_1-HE.noGEN.end.TE	percent
uq reads:	1929843	128038	6.6346%
   reads: 	2048101	135110	6.5968%
----------------
Candidate insertion sites in file: EB18_1-HE_insert.txt
  reads:	27060
  uqreads:	25998
  Number of Candidate sites:	25998

Level 1 collapse of insertion sites in file: EB18_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	545

Level 1 annotation file: EB18_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
EB18_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	EB18_1-HE.noGEN.front	EB18_1-HE.noGEN.front.gendel	percent
uq reads:	1929843	1107945	57.4111%
   reads: 	2048101	1140532	55.6873%
----------------
match_dm6_mask_gen_del:1:
  reads:	EB18_1-HE.noGEN.end	EB18_1-HE.noGEN.end.gendel	percent
uq reads:	1929843	950352	49.2450%
   reads: 	2048101	983357	48.0131%
----------------
Candidate breakpoint sites in file: EB18_1-HE_depletion.xls
  reads:	99089
  uqreads:	96182
  Number of reads supporting candidate sites:	96182

Level 1 collapse of depletion sites in file: EB18_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3380