Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-69.fastq.uq.polyn	RAL-69.filter	percent
uq reads:	31204617	2471172	7.9193%
   reads: 	33445813	2864131	8.5635%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-69.filter	RAL-69.nostrna	percent
uq reads:	2471172	1751663	70.8839%
   reads: 	2864131	1981907	69.1975%
----------------
TE_filter:
  reads:	RAL-69.nostrna	RAL-69.noTE	percent
uq reads:	1751663	1739278	99.2930%
   reads: 	1981907	1965922	99.1935%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-69.noGEN.front	RAL-69.noGEN.front.gen	percent
uq reads:	1739278	523510	30.0993%
   reads: 	1965922	664028	33.7769%
----------------
match_TE:2:
  reads:	RAL-69.noGEN.front	RAL-69.noGEN.front.TE	percent
uq reads:	1739278	87615	5.0374%
   reads: 	1965922	90868	4.6222%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-69.noGEN.end	RAL-69.noGEN.end.gen	percent
uq reads:	1739278	505610	29.0701%
   reads: 	1965922	631464	32.1205%
----------------
match_TE:2:
  reads:	RAL-69.noGEN.end	RAL-69.noGEN.end.TE	percent
uq reads:	1739278	88389	5.0819%
   reads: 	1965922	92268	4.6934%
----------------
Candidate insertion sites in file: RAL-69_insert.txt
  reads:	9930
  uqreads:	9731
  Number of Candidate sites:	9731

Level 1 collapse of insertion sites in file: RAL-69_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	451

Level 1 annotation file: RAL-69_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-69_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-69.noGEN.front	RAL-69.noGEN.front.gendel	percent
uq reads:	1739278	523510	30.0993%
   reads: 	1965922	664028	33.7769%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-69.noGEN.end	RAL-69.noGEN.end.gendel	percent
uq reads:	1739278	505610	29.0701%
   reads: 	1965922	631464	32.1205%
----------------
Candidate breakpoint sites in file: RAL-69_depletion.xls
  reads:	21261
  uqreads:	20607
  Number of reads supporting candidate sites:	20607

Level 1 collapse of depletion sites in file: RAL-69_depletion_level1.xls
  Number of Level 1 collapsed sites:	1517