Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-374.fastq.uq.polyn	RAL-374.filter	percent
uq reads:	25680383	2575912	10.0307%
   reads: 	27348439	3006401	10.9930%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-374.filter	RAL-374.nostrna	percent
uq reads:	2575912	1212292	47.0626%
   reads: 	3006401	1456492	48.4464%
----------------
TE_filter:
  reads:	RAL-374.nostrna	RAL-374.noTE	percent
uq reads:	1212292	1201950	99.1469%
   reads: 	1456492	1443466	99.1057%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-374.noGEN.front	RAL-374.noGEN.front.gen	percent
uq reads:	1201950	399133	33.2071%
   reads: 	1443466	518178	35.8982%
----------------
match_TE:2:
  reads:	RAL-374.noGEN.front	RAL-374.noGEN.front.TE	percent
uq reads:	1201950	65870	5.4803%
   reads: 	1443466	69429	4.8099%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-374.noGEN.end	RAL-374.noGEN.end.gen	percent
uq reads:	1201950	343094	28.5448%
   reads: 	1443466	453516	31.4185%
----------------
match_TE:2:
  reads:	RAL-374.noGEN.end	RAL-374.noGEN.end.TE	percent
uq reads:	1201950	62456	5.1962%
   reads: 	1443466	66472	4.6050%
----------------
Candidate insertion sites in file: RAL-374_insert.txt
  reads:	10376
  uqreads:	10230
  Number of Candidate sites:	10230

Level 1 collapse of insertion sites in file: RAL-374_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	555

Level 1 annotation file: RAL-374_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-374_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-374.noGEN.front	RAL-374.noGEN.front.gendel	percent
uq reads:	1201950	407467	33.9005%
   reads: 	1443466	534897	37.0564%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-374.noGEN.end	RAL-374.noGEN.end.gendel	percent
uq reads:	1201950	350078	29.1258%
   reads: 	1443466	468826	32.4792%
----------------
Candidate breakpoint sites in file: RAL-374_depletion.xls
  reads:	23292
  uqreads:	22857
  Number of reads supporting candidate sites:	22857

Level 1 collapse of depletion sites in file: RAL-374_depletion_level1.xls
  Number of Level 1 collapsed sites:	2210