Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-716.fastq.uq.polyn	RAL-716.filter	percent
uq reads:	29706022	2445860	8.2335%
   reads: 	31115469	2768560	8.8977%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-716.filter	RAL-716.nostrna	percent
uq reads:	2445860	1697841	69.4169%
   reads: 	2768560	1919947	69.3482%
----------------
TE_filter:
  reads:	RAL-716.nostrna	RAL-716.noTE	percent
uq reads:	1697841	1683396	99.1492%
   reads: 	1919947	1904287	99.1844%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-716.noGEN.front	RAL-716.noGEN.front.gen	percent
uq reads:	1683396	585752	34.7959%
   reads: 	1904287	728340	38.2474%
----------------
match_TE:2:
  reads:	RAL-716.noGEN.front	RAL-716.noGEN.front.TE	percent
uq reads:	1683396	74661	4.4351%
   reads: 	1904287	76165	3.9997%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-716.noGEN.end	RAL-716.noGEN.end.gen	percent
uq reads:	1683396	494483	29.3741%
   reads: 	1904287	632657	33.2228%
----------------
match_TE:2:
  reads:	RAL-716.noGEN.end	RAL-716.noGEN.end.TE	percent
uq reads:	1683396	76036	4.5168%
   reads: 	1904287	78409	4.1175%
----------------
Candidate insertion sites in file: RAL-716_insert.txt
  reads:	6807
  uqreads:	6670
  Number of Candidate sites:	6670

Level 1 collapse of insertion sites in file: RAL-716_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	381

Level 1 annotation file: RAL-716_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-716_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-716.noGEN.front	RAL-716.noGEN.front.gendel	percent
uq reads:	1683396	585752	34.7959%
   reads: 	1904287	728340	38.2474%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-716.noGEN.end	RAL-716.noGEN.end.gendel	percent
uq reads:	1683396	494483	29.3741%
   reads: 	1904287	632657	33.2228%
----------------
Candidate breakpoint sites in file: RAL-716_depletion.xls
  reads:	14622
  uqreads:	14131
  Number of reads supporting candidate sites:	14131

Level 1 collapse of depletion sites in file: RAL-716_depletion_level1.xls
  Number of Level 1 collapsed sites:	1247