Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-362_75b.fastq.uq.polyn	RAL-362_75b.filter	percent
uq reads:	18120624	4914377	27.1204%
   reads: 	19030367	5172169	27.1785%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-362_75b.filter	RAL-362_75b.nostrna	percent
uq reads:	4914377	4377291	89.0711%
   reads: 	5172169	4594202	88.8254%
----------------
TE_filter:
  reads:	RAL-362_75b.nostrna	RAL-362_75b.noTE	percent
uq reads:	4377291	4372677	99.8946%
   reads: 	4594202	4589115	99.8893%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-362_75b.noGEN.front	RAL-362_75b.noGEN.front.gen	percent
uq reads:	4372677	649079	14.8440%
   reads: 	4589115	740112	16.1276%
----------------
match_TE:2:
  reads:	RAL-362_75b.noGEN.front	RAL-362_75b.noGEN.front.TE	percent
uq reads:	4372677	98901	2.2618%
   reads: 	4589115	102178	2.2265%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-362_75b.noGEN.end	RAL-362_75b.noGEN.end.gen	percent
uq reads:	4372677	206099	4.7133%
   reads: 	4589115	298252	6.4991%
----------------
match_TE:2:
  reads:	RAL-362_75b.noGEN.end	RAL-362_75b.noGEN.end.TE	percent
uq reads:	4372677	46315	1.0592%
   reads: 	4589115	49722	1.0835%
----------------
Candidate insertion sites in file: RAL-362_75b_insert.txt
  reads:	3758
  uqreads:	3713
  Number of Candidate sites:	3713

Level 1 collapse of insertion sites in file: RAL-362_75b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	230

Level 1 annotation file: RAL-362_75b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-362_75b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-362_75b.noGEN.front	RAL-362_75b.noGEN.front.gendel	percent
uq reads:	4372677	649079	14.8440%
   reads: 	4589115	740112	16.1276%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-362_75b.noGEN.end	RAL-362_75b.noGEN.end.gendel	percent
uq reads:	4372677	206099	4.7133%
   reads: 	4589115	298252	6.4991%
----------------
Candidate breakpoint sites in file: RAL-362_75b_depletion.xls
  reads:	8386
  uqreads:	8063
  Number of reads supporting candidate sites:	8063

Level 1 collapse of depletion sites in file: RAL-362_75b_depletion_level1.xls
  Number of Level 1 collapsed sites:	599