Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-757.fastq.uq.polyn	RAL-757.filter	percent
uq reads:	67152085	6080833	9.0553%
   reads: 	72612703	6867318	9.4575%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-757.filter	RAL-757.nostrna	percent
uq reads:	6080833	5681933	93.4400%
   reads: 	6867318	6292952	91.6362%
----------------
TE_filter:
  reads:	RAL-757.nostrna	RAL-757.noTE	percent
uq reads:	5681933	5653119	99.4929%
   reads: 	6292952	6258979	99.4601%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-757.noGEN.front	RAL-757.noGEN.front.gen	percent
uq reads:	5653119	1598443	28.2754%
   reads: 	6258979	1839827	29.3950%
----------------
match_TE:2:
  reads:	RAL-757.noGEN.front	RAL-757.noGEN.front.TE	percent
uq reads:	5653119	181076	3.2031%
   reads: 	6258979	189545	3.0284%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-757.noGEN.end	RAL-757.noGEN.end.gen	percent
uq reads:	5653119	1240957	21.9517%
   reads: 	6258979	1470519	23.4946%
----------------
match_TE:2:
  reads:	RAL-757.noGEN.end	RAL-757.noGEN.end.TE	percent
uq reads:	5653119	172570	3.0527%
   reads: 	6258979	183716	2.9352%
----------------
Candidate insertion sites in file: RAL-757_insert.txt
  reads:	17977
  uqreads:	17637
  Number of Candidate sites:	17637

Level 1 collapse of insertion sites in file: RAL-757_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	676

Level 1 annotation file: RAL-757_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-757_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-757.noGEN.front	RAL-757.noGEN.front.gendel	percent
uq reads:	5653119	1622778	28.7059%
   reads: 	6258979	1871512	29.9012%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-757.noGEN.end	RAL-757.noGEN.end.gendel	percent
uq reads:	5653119	1262881	22.3395%
   reads: 	6258979	1499964	23.9650%
----------------
Candidate breakpoint sites in file: RAL-757_depletion.xls
  reads:	33777
  uqreads:	32168
  Number of reads supporting candidate sites:	32168

Level 1 collapse of depletion sites in file: RAL-757_depletion_level1.xls
  Number of Level 1 collapsed sites:	2570