Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-774_125.fastq.uq.polyn	RAL-774_125.filter	percent
uq reads:	31268949	4392109	14.0462%
   reads: 	33176896	4772163	14.3840%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-774_125.filter	RAL-774_125.nostrna	percent
uq reads:	4392109	4295025	97.7896%
   reads: 	4772163	4628085	96.9809%
----------------
TE_filter:
  reads:	RAL-774_125.nostrna	RAL-774_125.noTE	percent
uq reads:	4295025	4289218	99.8648%
   reads: 	4628085	4621778	99.8637%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-774_125.noGEN.front	RAL-774_125.noGEN.front.gen	percent
uq reads:	4289218	1476757	34.4295%
   reads: 	4621778	1576932	34.1196%
----------------
match_TE:2:
  reads:	RAL-774_125.noGEN.front	RAL-774_125.noGEN.front.TE	percent
uq reads:	4289218	221854	5.1724%
   reads: 	4621778	225940	4.8886%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-774_125.noGEN.end	RAL-774_125.noGEN.end.gen	percent
uq reads:	4289218	307510	7.1694%
   reads: 	4621778	402410	8.7068%
----------------
match_TE:2:
  reads:	RAL-774_125.noGEN.end	RAL-774_125.noGEN.end.TE	percent
uq reads:	4289218	70877	1.6524%
   reads: 	4621778	74636	1.6149%
----------------
Candidate insertion sites in file: RAL-774_125_insert.txt
  reads:	14178
  uqreads:	13944
  Number of Candidate sites:	13944

Level 1 collapse of insertion sites in file: RAL-774_125_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	590

Level 1 annotation file: RAL-774_125_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-774_125_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-774_125.noGEN.front	RAL-774_125.noGEN.front.gendel	percent
uq reads:	4289218	1476757	34.4295%
   reads: 	4621778	1576932	34.1196%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-774_125.noGEN.end	RAL-774_125.noGEN.end.gendel	percent
uq reads:	4289218	307510	7.1694%
   reads: 	4621778	402410	8.7068%
----------------
Candidate breakpoint sites in file: RAL-774_125_depletion.xls
  reads:	35839
  uqreads:	35109
  Number of reads supporting candidate sites:	35109

Level 1 collapse of depletion sites in file: RAL-774_125_depletion_level1.xls
  Number of Level 1 collapsed sites:	2994