Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-820.fastq.uq.polyn	RAL-820.filter	percent
uq reads:	34706826	4643836	13.3802%
   reads: 	36876427	5149417	13.9640%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-820.filter	RAL-820.nostrna	percent
uq reads:	4643836	3452536	74.3466%
   reads: 	5149417	3794454	73.6871%
----------------
TE_filter:
  reads:	RAL-820.nostrna	RAL-820.noTE	percent
uq reads:	3452536	3440395	99.6483%
   reads: 	3794454	3778931	99.5909%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-820.noGEN.front	RAL-820.noGEN.front.gen	percent
uq reads:	3440395	1559195	45.3202%
   reads: 	3778931	1761426	46.6118%
----------------
match_TE:2:
  reads:	RAL-820.noGEN.front	RAL-820.noGEN.front.TE	percent
uq reads:	3440395	212697	6.1823%
   reads: 	3778931	217217	5.7481%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-820.noGEN.end	RAL-820.noGEN.end.gen	percent
uq reads:	3440395	533451	15.5055%
   reads: 	3778931	720759	19.0731%
----------------
match_TE:2:
  reads:	RAL-820.noGEN.end	RAL-820.noGEN.end.TE	percent
uq reads:	3440395	100824	2.9306%
   reads: 	3778931	105897	2.8023%
----------------
Candidate insertion sites in file: RAL-820_insert.txt
  reads:	9091
  uqreads:	8921
  Number of Candidate sites:	8921

Level 1 collapse of insertion sites in file: RAL-820_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	497

Level 1 annotation file: RAL-820_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-820_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-820.noGEN.front	RAL-820.noGEN.front.gendel	percent
uq reads:	3440395	1559195	45.3202%
   reads: 	3778931	1761426	46.6118%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-820.noGEN.end	RAL-820.noGEN.end.gendel	percent
uq reads:	3440395	533451	15.5055%
   reads: 	3778931	720759	19.0731%
----------------
Candidate breakpoint sites in file: RAL-820_depletion.xls
  reads:	18752
  uqreads:	17922
  Number of reads supporting candidate sites:	17922

Level 1 collapse of depletion sites in file: RAL-820_depletion_level1.xls
  Number of Level 1 collapsed sites:	1795