Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-42.fastq.uq.polyn	RAL-42.filter	percent
uq reads:	32915793	2778240	8.4404%
   reads: 	36651726	3788044	10.3352%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-42.filter	RAL-42.nostrna	percent
uq reads:	2778240	2698278	97.1218%
   reads: 	3788044	3584504	94.6268%
----------------
TE_filter:
  reads:	RAL-42.nostrna	RAL-42.noTE	percent
uq reads:	2698278	2693617	99.8273%
   reads: 	3584504	3579696	99.8659%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-42.noGEN.front	RAL-42.noGEN.front.gen	percent
uq reads:	2693617	829121	30.7810%
   reads: 	3579696	939506	26.2454%
----------------
match_TE:2:
  reads:	RAL-42.noGEN.front	RAL-42.noGEN.front.TE	percent
uq reads:	2693617	139116	5.1647%
   reads: 	3579696	142393	3.9778%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-42.noGEN.end	RAL-42.noGEN.end.gen	percent
uq reads:	2693617	737417	27.3765%
   reads: 	3579696	834090	23.3006%
----------------
match_TE:2:
  reads:	RAL-42.noGEN.end	RAL-42.noGEN.end.TE	percent
uq reads:	2693617	148446	5.5110%
   reads: 	3579696	152154	4.2505%
----------------
Candidate insertion sites in file: RAL-42_insert.txt
  reads:	22701
  uqreads:	22465
  Number of Candidate sites:	22465

Level 1 collapse of insertion sites in file: RAL-42_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	498

Level 1 annotation file: RAL-42_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-42_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-42.noGEN.front	RAL-42.noGEN.front.gendel	percent
uq reads:	2693617	845353	31.3836%
   reads: 	3579696	957591	26.7506%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-42.noGEN.end	RAL-42.noGEN.end.gendel	percent
uq reads:	2693617	752907	27.9515%
   reads: 	3579696	851408	23.7844%
----------------
Candidate breakpoint sites in file: RAL-42_depletion.xls
  reads:	40466
  uqreads:	39566
  Number of reads supporting candidate sites:	39566

Level 1 collapse of depletion sites in file: RAL-42_depletion_level1.xls
  Number of Level 1 collapsed sites:	2027