Insertion Pipeline
Bowtie2_wholegenome:
  reads:	UG28N_1-HE.fastq.uq.polyn	UG28N_1-HE.filter	percent
uq reads:	58095238	2712889	4.6697%
   reads: 	65530773	2982630	4.5515%
----------------
virus_structural_rna_repbase_filter:
  reads:	UG28N_1-HE.filter	UG28N_1-HE.nostrna	percent
uq reads:	2712889	2327114	85.7799%
   reads: 	2982630	2555281	85.6721%
----------------
TE_filter:
  reads:	UG28N_1-HE.nostrna	UG28N_1-HE.noTE	percent
uq reads:	2327114	2316304	99.5355%
   reads: 	2555281	2534508	99.1871%
----------------
match_dm6_mask_gen:1:
  reads:	UG28N_1-HE.noGEN.front	UG28N_1-HE.noGEN.front.gen	percent
uq reads:	2316304	1159205	50.0455%
   reads: 	2534508	1249577	49.3025%
----------------
match_TE:2:
  reads:	UG28N_1-HE.noGEN.front	UG28N_1-HE.noGEN.front.TE	percent
uq reads:	2316304	84770	3.6597%
   reads: 	2534508	92379	3.6448%
----------------
match_dm6_mask_gen:1:
  reads:	UG28N_1-HE.noGEN.end	UG28N_1-HE.noGEN.end.gen	percent
uq reads:	2316304	1193986	51.5470%
   reads: 	2534508	1293941	51.0529%
----------------
match_TE:2:
  reads:	UG28N_1-HE.noGEN.end	UG28N_1-HE.noGEN.end.TE	percent
uq reads:	2316304	83114	3.5882%
   reads: 	2534508	90542	3.5724%
----------------
Candidate insertion sites in file: UG28N_1-HE_insert.txt
  reads:	17839
  uqreads:	16245
  Number of Candidate sites:	16245

Level 1 collapse of insertion sites in file: UG28N_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	546

Level 1 annotation file: UG28N_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
UG28N_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	UG28N_1-HE.noGEN.front	UG28N_1-HE.noGEN.front.gendel	percent
uq reads:	2316304	1159205	50.0455%
   reads: 	2534508	1249577	49.3025%
----------------
match_dm6_mask_gen_del:1:
  reads:	UG28N_1-HE.noGEN.end	UG28N_1-HE.noGEN.end.gendel	percent
uq reads:	2316304	1193986	51.5470%
   reads: 	2534508	1293941	51.0529%
----------------
Candidate breakpoint sites in file: UG28N_1-HE_depletion.xls
  reads:	64058
  uqreads:	58025
  Number of reads supporting candidate sites:	58025

Level 1 collapse of depletion sites in file: UG28N_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3697