Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-508.fastq.uq.polyn	RAL-508.filter	percent
uq reads:	38827625	2376168	6.1198%
   reads: 	41562857	2857928	6.8762%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-508.filter	RAL-508.nostrna	percent
uq reads:	2376168	2290181	96.3813%
   reads: 	2857928	2741240	95.9170%
----------------
TE_filter:
  reads:	RAL-508.nostrna	RAL-508.noTE	percent
uq reads:	2290181	2272502	99.2281%
   reads: 	2741240	2722181	99.3047%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-508.noGEN.front	RAL-508.noGEN.front.gen	percent
uq reads:	2272502	745006	32.7835%
   reads: 	2722181	985298	36.1952%
----------------
match_TE:2:
  reads:	RAL-508.noGEN.front	RAL-508.noGEN.front.TE	percent
uq reads:	2272502	124038	5.4582%
   reads: 	2722181	128120	4.7065%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-508.noGEN.end	RAL-508.noGEN.end.gen	percent
uq reads:	2272502	594604	26.1652%
   reads: 	2722181	813651	29.8897%
----------------
match_TE:2:
  reads:	RAL-508.noGEN.end	RAL-508.noGEN.end.TE	percent
uq reads:	2272502	117001	5.1486%
   reads: 	2722181	122971	4.5174%
----------------
Candidate insertion sites in file: RAL-508_insert.txt
  reads:	16641
  uqreads:	16401
  Number of Candidate sites:	16401

Level 1 collapse of insertion sites in file: RAL-508_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	573

Level 1 annotation file: RAL-508_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-508_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-508.noGEN.front	RAL-508.noGEN.front.gendel	percent
uq reads:	2272502	759703	33.4302%
   reads: 	2722181	1005901	36.9520%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-508.noGEN.end	RAL-508.noGEN.end.gendel	percent
uq reads:	2272502	606898	26.7062%
   reads: 	2722181	831861	30.5586%
----------------
Candidate breakpoint sites in file: RAL-508_depletion.xls
  reads:	37226
  uqreads:	36363
  Number of reads supporting candidate sites:	36363

Level 1 collapse of depletion sites in file: RAL-508_depletion_level1.xls
  Number of Level 1 collapsed sites:	2798