Insertion Pipeline
Bowtie2_wholegenome:
  reads:	Cl.8.fastq.uq.polyn	Cl.8.filter	percent
uq reads:	29797698	0	0.0000%
   reads: 	37270617		0.0000%
----------------
virus_structural_rna_repbase_filter:
  reads:	Cl.8.filter	Cl.8.nostrna	percent
uq reads:	0	0	%
   reads: 			%
----------------
TE_filter:
  reads:	Cl.8.nostrna	Cl.8.noTE	percent
uq reads:	0	0	%
   reads: 			%
----------------
match_dm6_mask_gen:1:
  reads:	Cl.8.noGEN.front	Cl.8.noGEN.front.gen	percent
uq reads:	0	0	%
   reads: 			%
----------------
match_TE:2:
  reads:	Cl.8.noGEN.front	Cl.8.noGEN.front.TE	percent
uq reads:	0	0	%
   reads: 			%
----------------
match_dm6_mask_gen:1:
  reads:	Cl.8.noGEN.end	Cl.8.noGEN.end.gen	percent
uq reads:	0	0	%
   reads: 			%
----------------
match_TE:2:
  reads:	Cl.8.noGEN.end	Cl.8.noGEN.end.TE	percent
uq reads:	0	0	%
   reads: 			%
----------------
Candidate insertion sites in file: Cl.8_insert.txt
  reads:	
  uqreads:	0
  Number of Candidate sites:	0

Level 1 collapse of insertion sites in file: Cl.8_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1

Level 1 annotation file: Cl.8_level1siteannotation.xls
Insertion sites in fixed bin:
Cl.8_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	Cl.8.noGEN.front	Cl.8.noGEN.front.gendel	percent
uq reads:	0	0	%
   reads: 			%
----------------
match_dm6_mask_gen_del:1:
  reads:	Cl.8.noGEN.end	Cl.8.noGEN.end.gendel	percent
uq reads:	0	0	%
   reads: 			%
----------------
Candidate breakpoint sites in file: Cl.8_depletion.xls
  reads:	
  uqreads:	0
  Number of reads supporting candidate sites:	0

Level 1 collapse of depletion sites in file: Cl.8_depletion_level1.xls
  Number of Level 1 collapsed sites:	1