Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-843.fastq.uq.polyn	RAL-843.filter	percent
uq reads:	60440726	7759097	12.8375%
   reads: 	67799767	9332203	13.7644%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-843.filter	RAL-843.nostrna	percent
uq reads:	7759097	7687500	99.0773%
   reads: 	9332203	9081912	97.3180%
----------------
TE_filter:
  reads:	RAL-843.nostrna	RAL-843.noTE	percent
uq reads:	7687500	7673814	99.8220%
   reads: 	9081912	9057382	99.7299%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-843.noGEN.front	RAL-843.noGEN.front.gen	percent
uq reads:	7673814	1640576	21.3789%
   reads: 	9057382	1933193	21.3438%
----------------
match_TE:2:
  reads:	RAL-843.noGEN.front	RAL-843.noGEN.front.TE	percent
uq reads:	7673814	249123	3.2464%
   reads: 	9057382	272129	3.0045%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-843.noGEN.end	RAL-843.noGEN.end.gen	percent
uq reads:	7673814	1049402	13.6751%
   reads: 	9057382	1332261	14.7091%
----------------
match_TE:2:
  reads:	RAL-843.noGEN.end	RAL-843.noGEN.end.TE	percent
uq reads:	7673814	179923	2.3446%
   reads: 	9057382	202574	2.2366%
----------------
Candidate insertion sites in file: RAL-843_insert.txt
  reads:	43534
  uqreads:	41727
  Number of Candidate sites:	41727

Level 1 collapse of insertion sites in file: RAL-843_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	674

Level 1 annotation file: RAL-843_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-843_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-843.noGEN.front	RAL-843.noGEN.front.gendel	percent
uq reads:	7673814	1640576	21.3789%
   reads: 	9057382	1933193	21.3438%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-843.noGEN.end	RAL-843.noGEN.end.gendel	percent
uq reads:	7673814	1049402	13.6751%
   reads: 	9057382	1332261	14.7091%
----------------
Candidate breakpoint sites in file: RAL-843_depletion.xls
  reads:	105413
  uqreads:	100167
  Number of reads supporting candidate sites:	100167

Level 1 collapse of depletion sites in file: RAL-843_depletion_level1.xls
  Number of Level 1 collapsed sites:	4008