Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-892.fastq.uq.polyn	RAL-892.filter	percent
uq reads:	40542891	6065260	14.9601%
   reads: 	44994246	8034724	17.8572%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-892.filter	RAL-892.nostrna	percent
uq reads:	6065260	3020387	49.7981%
   reads: 	8034724	3608192	44.9075%
----------------
TE_filter:
  reads:	RAL-892.nostrna	RAL-892.noTE	percent
uq reads:	3020387	3007279	99.5660%
   reads: 	3608192	3591900	99.5485%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-892.noGEN.front	RAL-892.noGEN.front.gen	percent
uq reads:	3007279	813450	27.0494%
   reads: 	3591900	954400	26.5709%
----------------
match_TE:2:
  reads:	RAL-892.noGEN.front	RAL-892.noGEN.front.TE	percent
uq reads:	3007279	123636	4.1112%
   reads: 	3591900	135768	3.7798%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-892.noGEN.end	RAL-892.noGEN.end.gen	percent
uq reads:	3007279	561942	18.6861%
   reads: 	3591900	687961	19.1531%
----------------
match_TE:2:
  reads:	RAL-892.noGEN.end	RAL-892.noGEN.end.TE	percent
uq reads:	3007279	105990	3.5244%
   reads: 	3591900	119472	3.3262%
----------------
Candidate insertion sites in file: RAL-892_insert.txt
  reads:	15243
  uqreads:	14717
  Number of Candidate sites:	14717

Level 1 collapse of insertion sites in file: RAL-892_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	603

Level 1 annotation file: RAL-892_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-892_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-892.noGEN.front	RAL-892.noGEN.front.gendel	percent
uq reads:	3007279	828215	27.5403%
   reads: 	3591900	972356	27.0708%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-892.noGEN.end	RAL-892.noGEN.end.gendel	percent
uq reads:	3007279	572763	19.0459%
   reads: 	3591900	701662	19.5346%
----------------
Candidate breakpoint sites in file: RAL-892_depletion.xls
  reads:	35212
  uqreads:	33810
  Number of reads supporting candidate sites:	33810

Level 1 collapse of depletion sites in file: RAL-892_depletion_level1.xls
  Number of Level 1 collapsed sites:	2844