Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-392.fastq.uq.polyn	RAL-392.filter	percent
uq reads:	43809088	2826155	6.4511%
   reads: 	49092607	3888932	7.9216%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-392.filter	RAL-392.nostrna	percent
uq reads:	2826155	2639753	93.4044%
   reads: 	3888932	3482924	89.5599%
----------------
TE_filter:
  reads:	RAL-392.nostrna	RAL-392.noTE	percent
uq reads:	2639753	2628915	99.5894%
   reads: 	3482924	3470381	99.6399%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-392.noGEN.front	RAL-392.noGEN.front.gen	percent
uq reads:	2628915	596293	22.6821%
   reads: 	3470381	780799	22.4989%
----------------
match_TE:2:
  reads:	RAL-392.noGEN.front	RAL-392.noGEN.front.TE	percent
uq reads:	2628915	84681	3.2211%
   reads: 	3470381	99013	2.8531%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-392.noGEN.end	RAL-392.noGEN.end.gen	percent
uq reads:	2628915	553463	21.0529%
   reads: 	3470381	736743	21.2295%
----------------
match_TE:2:
  reads:	RAL-392.noGEN.end	RAL-392.noGEN.end.TE	percent
uq reads:	2628915	83702	3.1839%
   reads: 	3470381	99109	2.8559%
----------------
Candidate insertion sites in file: RAL-392_insert.txt
  reads:	11945
  uqreads:	11686
  Number of Candidate sites:	11686

Level 1 collapse of insertion sites in file: RAL-392_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	573

Level 1 annotation file: RAL-392_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-392_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-392.noGEN.front	RAL-392.noGEN.front.gendel	percent
uq reads:	2628915	605568	23.0349%
   reads: 	3470381	793346	22.8605%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-392.noGEN.end	RAL-392.noGEN.end.gendel	percent
uq reads:	2628915	562198	21.3852%
   reads: 	3470381	748283	21.5620%
----------------
Candidate breakpoint sites in file: RAL-392_depletion.xls
  reads:	32089
  uqreads:	31150
  Number of reads supporting candidate sites:	31150

Level 1 collapse of depletion sites in file: RAL-392_depletion_level1.xls
  Number of Level 1 collapsed sites:	2668