Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-149.fastq.uq.polyn	RAL-149.filter	percent
uq reads:	39291883	3734133	9.5036%
   reads: 	40293426	3923755	9.7380%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-149.filter	RAL-149.nostrna	percent
uq reads:	3734133	2101170	56.2693%
   reads: 	3923755	2242800	57.1595%
----------------
TE_filter:
  reads:	RAL-149.nostrna	RAL-149.noTE	percent
uq reads:	2101170	2082475	99.1103%
   reads: 	2242800	2223191	99.1257%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-149.noGEN.front	RAL-149.noGEN.front.gen	percent
uq reads:	2082475	774937	37.2123%
   reads: 	2223191	855707	38.4900%
----------------
match_TE:2:
  reads:	RAL-149.noGEN.front	RAL-149.noGEN.front.TE	percent
uq reads:	2082475	93383	4.4842%
   reads: 	2223191	94361	4.2444%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-149.noGEN.end	RAL-149.noGEN.end.gen	percent
uq reads:	2082475	640389	30.7513%
   reads: 	2223191	714858	32.1546%
----------------
match_TE:2:
  reads:	RAL-149.noGEN.end	RAL-149.noGEN.end.TE	percent
uq reads:	2082475	83627	4.0158%
   reads: 	2223191	84779	3.8134%
----------------
Candidate insertion sites in file: RAL-149_insert.txt
  reads:	6583
  uqreads:	6564
  Number of Candidate sites:	6564

Level 1 collapse of insertion sites in file: RAL-149_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	397

Level 1 annotation file: RAL-149_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-149_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-149.noGEN.front	RAL-149.noGEN.front.gendel	percent
uq reads:	2082475	774937	37.2123%
   reads: 	2223191	855707	38.4900%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-149.noGEN.end	RAL-149.noGEN.end.gendel	percent
uq reads:	2082475	640389	30.7513%
   reads: 	2223191	714858	32.1546%
----------------
Candidate breakpoint sites in file: RAL-149_depletion.xls
  reads:	14453
  uqreads:	14349
  Number of reads supporting candidate sites:	14349

Level 1 collapse of depletion sites in file: RAL-149_depletion_level1.xls
  Number of Level 1 collapsed sites:	1229