Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-109_75b.fastq.uq.polyn	RAL-109_75b.filter	percent
uq reads:	27578179	2308728	8.3716%
   reads: 	28622445	2712792	9.4778%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-109_75b.filter	RAL-109_75b.nostrna	percent
uq reads:	2308728	2259225	97.8558%
   reads: 	2712792	2661496	98.1091%
----------------
TE_filter:
  reads:	RAL-109_75b.nostrna	RAL-109_75b.noTE	percent
uq reads:	2259225	2247657	99.4880%
   reads: 	2661496	2649455	99.5476%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-109_75b.noGEN.front	RAL-109_75b.noGEN.front.gen	percent
uq reads:	2247657	560760	24.9486%
   reads: 	2649455	845876	31.9264%
----------------
match_TE:2:
  reads:	RAL-109_75b.noGEN.front	RAL-109_75b.noGEN.front.TE	percent
uq reads:	2247657	56487	2.5132%
   reads: 	2649455	57600	2.1740%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-109_75b.noGEN.end	RAL-109_75b.noGEN.end.gen	percent
uq reads:	2247657	439405	19.5495%
   reads: 	2649455	713172	26.9177%
----------------
match_TE:2:
  reads:	RAL-109_75b.noGEN.end	RAL-109_75b.noGEN.end.TE	percent
uq reads:	2247657	49656	2.2092%
   reads: 	2649455	50760	1.9159%
----------------
Candidate insertion sites in file: RAL-109_75b_insert.txt
  reads:	3736
  uqreads:	3705
  Number of Candidate sites:	3705

Level 1 collapse of insertion sites in file: RAL-109_75b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	259

Level 1 annotation file: RAL-109_75b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-109_75b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-109_75b.noGEN.front	RAL-109_75b.noGEN.front.gendel	percent
uq reads:	2247657	560760	24.9486%
   reads: 	2649455	845876	31.9264%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-109_75b.noGEN.end	RAL-109_75b.noGEN.end.gendel	percent
uq reads:	2247657	439405	19.5495%
   reads: 	2649455	713172	26.9177%
----------------
Candidate breakpoint sites in file: RAL-109_75b_depletion.xls
  reads:	9261
  uqreads:	9081
  Number of reads supporting candidate sites:	9081

Level 1 collapse of depletion sites in file: RAL-109_75b_depletion_level1.xls
  Number of Level 1 collapsed sites:	643