Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-535.fastq.uq.polyn	RAL-535.filter	percent
uq reads:	37501261	4474450	11.9315%
   reads: 	39576860	4872298	12.3110%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-535.filter	RAL-535.nostrna	percent
uq reads:	4474450	3147400	70.3416%
   reads: 	4872298	3379958	69.3709%
----------------
TE_filter:
  reads:	RAL-535.nostrna	RAL-535.noTE	percent
uq reads:	3147400	3133108	99.5459%
   reads: 	3379958	3363924	99.5256%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-535.noGEN.front	RAL-535.noGEN.front.gen	percent
uq reads:	3133108	697149	22.2510%
   reads: 	3363924	812653	24.1579%
----------------
match_TE:2:
  reads:	RAL-535.noGEN.front	RAL-535.noGEN.front.TE	percent
uq reads:	3133108	99476	3.1750%
   reads: 	3363924	107070	3.1829%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-535.noGEN.end	RAL-535.noGEN.end.gen	percent
uq reads:	3133108	575586	18.3711%
   reads: 	3363924	685905	20.3900%
----------------
match_TE:2:
  reads:	RAL-535.noGEN.end	RAL-535.noGEN.end.TE	percent
uq reads:	3133108	103042	3.2888%
   reads: 	3363924	111072	3.3019%
----------------
Candidate insertion sites in file: RAL-535_insert.txt
  reads:	9207
  uqreads:	9062
  Number of Candidate sites:	9062

Level 1 collapse of insertion sites in file: RAL-535_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	450

Level 1 annotation file: RAL-535_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-535_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-535.noGEN.front	RAL-535.noGEN.front.gendel	percent
uq reads:	3133108	697149	22.2510%
   reads: 	3363924	812653	24.1579%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-535.noGEN.end	RAL-535.noGEN.end.gendel	percent
uq reads:	3133108	575586	18.3711%
   reads: 	3363924	685905	20.3900%
----------------
Candidate breakpoint sites in file: RAL-535_depletion.xls
  reads:	20415
  uqreads:	19917
  Number of reads supporting candidate sites:	19917

Level 1 collapse of depletion sites in file: RAL-535_depletion_level1.xls
  Number of Level 1 collapsed sites:	1727