Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-142.fastq.uq.polyn	RAL-142.filter	percent
uq reads:	39089173	3088698	7.9017%
   reads: 	40436288	3281014	8.1140%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-142.filter	RAL-142.nostrna	percent
uq reads:	3088698	2784205	90.1417%
   reads: 	3281014	2966283	90.4075%
----------------
TE_filter:
  reads:	RAL-142.nostrna	RAL-142.noTE	percent
uq reads:	2784205	2772722	99.5876%
   reads: 	2966283	2954551	99.6045%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-142.noGEN.front	RAL-142.noGEN.front.gen	percent
uq reads:	2772722	1064634	38.3967%
   reads: 	2954551	1146020	38.7883%
----------------
match_TE:2:
  reads:	RAL-142.noGEN.front	RAL-142.noGEN.front.TE	percent
uq reads:	2772722	160527	5.7895%
   reads: 	2954551	163182	5.5231%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-142.noGEN.end	RAL-142.noGEN.end.gen	percent
uq reads:	2772722	849872	30.6512%
   reads: 	2954551	927245	31.3836%
----------------
match_TE:2:
  reads:	RAL-142.noGEN.end	RAL-142.noGEN.end.TE	percent
uq reads:	2772722	148191	5.3446%
   reads: 	2954551	151208	5.1178%
----------------
Candidate insertion sites in file: RAL-142_insert.txt
  reads:	22485
  uqreads:	22405
  Number of Candidate sites:	22405

Level 1 collapse of insertion sites in file: RAL-142_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	548

Level 1 annotation file: RAL-142_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-142_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-142.noGEN.front	RAL-142.noGEN.front.gendel	percent
uq reads:	2772722	1064634	38.3967%
   reads: 	2954551	1146020	38.7883%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-142.noGEN.end	RAL-142.noGEN.end.gendel	percent
uq reads:	2772722	849872	30.6512%
   reads: 	2954551	927245	31.3836%
----------------
Candidate breakpoint sites in file: RAL-142_depletion.xls
  reads:	50335
  uqreads:	49809
  Number of reads supporting candidate sites:	49809

Level 1 collapse of depletion sites in file: RAL-142_depletion_level1.xls
  Number of Level 1 collapsed sites:	2684