Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-136.fastq.uq.polyn	RAL-136.filter	percent
uq reads:	37396553	4464433	11.9381%
   reads: 	38630081	4740109	12.2705%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-136.filter	RAL-136.nostrna	percent
uq reads:	4464433	3455307	77.3963%
   reads: 	4740109	3687731	77.7984%
----------------
TE_filter:
  reads:	RAL-136.nostrna	RAL-136.noTE	percent
uq reads:	3455307	3432981	99.3539%
   reads: 	3687731	3663766	99.3501%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-136.noGEN.front	RAL-136.noGEN.front.gen	percent
uq reads:	3432981	712872	20.7654%
   reads: 	3663766	851576	23.2432%
----------------
match_TE:2:
  reads:	RAL-136.noGEN.front	RAL-136.noGEN.front.TE	percent
uq reads:	3432981	90315	2.6308%
   reads: 	3663766	92090	2.5135%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-136.noGEN.end	RAL-136.noGEN.end.gen	percent
uq reads:	3432981	587333	17.1085%
   reads: 	3663766	714050	19.4895%
----------------
match_TE:2:
  reads:	RAL-136.noGEN.end	RAL-136.noGEN.end.TE	percent
uq reads:	3432981	84241	2.4539%
   reads: 	3663766	86435	2.3592%
----------------
Candidate insertion sites in file: RAL-136_insert.txt
  reads:	7733
  uqreads:	7676
  Number of Candidate sites:	7676

Level 1 collapse of insertion sites in file: RAL-136_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	520

Level 1 annotation file: RAL-136_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-136_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-136.noGEN.front	RAL-136.noGEN.front.gendel	percent
uq reads:	3432981	712872	20.7654%
   reads: 	3663766	851576	23.2432%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-136.noGEN.end	RAL-136.noGEN.end.gendel	percent
uq reads:	3432981	587333	17.1085%
   reads: 	3663766	714050	19.4895%
----------------
Candidate breakpoint sites in file: RAL-136_depletion.xls
  reads:	17403
  uqreads:	17123
  Number of reads supporting candidate sites:	17123

Level 1 collapse of depletion sites in file: RAL-136_depletion_level1.xls
  Number of Level 1 collapsed sites:	1484