Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-492.fastq.uq.polyn	RAL-492.filter	percent
uq reads:	41697238	2432289	5.8332%
   reads: 	44005846	2994618	6.8050%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-492.filter	RAL-492.nostrna	percent
uq reads:	2432289	2359383	97.0026%
   reads: 	2994618	2904706	96.9975%
----------------
TE_filter:
  reads:	RAL-492.nostrna	RAL-492.noTE	percent
uq reads:	2359383	2338241	99.1039%
   reads: 	2904706	2880199	99.1563%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-492.noGEN.front	RAL-492.noGEN.front.gen	percent
uq reads:	2338241	798241	34.1385%
   reads: 	2880199	1076026	37.3594%
----------------
match_TE:2:
  reads:	RAL-492.noGEN.front	RAL-492.noGEN.front.TE	percent
uq reads:	2338241	132462	5.6650%
   reads: 	2880199	136852	4.7515%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-492.noGEN.end	RAL-492.noGEN.end.gen	percent
uq reads:	2338241	617107	26.3919%
   reads: 	2880199	873572	30.3303%
----------------
match_TE:2:
  reads:	RAL-492.noGEN.end	RAL-492.noGEN.end.TE	percent
uq reads:	2338241	121449	5.1940%
   reads: 	2880199	128023	4.4449%
----------------
Candidate insertion sites in file: RAL-492_insert.txt
  reads:	14470
  uqreads:	14202
  Number of Candidate sites:	14202

Level 1 collapse of insertion sites in file: RAL-492_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	561

Level 1 annotation file: RAL-492_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-492_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-492.noGEN.front	RAL-492.noGEN.front.gendel	percent
uq reads:	2338241	816678	34.9270%
   reads: 	2880199	1110044	38.5405%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-492.noGEN.end	RAL-492.noGEN.end.gendel	percent
uq reads:	2338241	631289	26.9985%
   reads: 	2880199	903696	31.3762%
----------------
Candidate breakpoint sites in file: RAL-492_depletion.xls
  reads:	34743
  uqreads:	33828
  Number of reads supporting candidate sites:	33828

Level 1 collapse of depletion sites in file: RAL-492_depletion_level1.xls
  Number of Level 1 collapsed sites:	2851