Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-287.fastq.uq.polyn	RAL-287.filter	percent
uq reads:	32482494	9401018	28.9418%
   reads: 	33334755	9551532	28.6534%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-287.filter	RAL-287.nostrna	percent
uq reads:	9401018	8909487	94.7715%
   reads: 	9551532	9052614	94.7766%
----------------
TE_filter:
  reads:	RAL-287.nostrna	RAL-287.noTE	percent
uq reads:	8909487	8892352	99.8077%
   reads: 	9052614	9034484	99.7997%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-287.noGEN.front	RAL-287.noGEN.front.gen	percent
uq reads:	8892352	955976	10.7505%
   reads: 	9034484	1024879	11.3441%
----------------
match_TE:2:
  reads:	RAL-287.noGEN.front	RAL-287.noGEN.front.TE	percent
uq reads:	8892352	146554	1.6481%
   reads: 	9034484	147162	1.6289%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-287.noGEN.end	RAL-287.noGEN.end.gen	percent
uq reads:	8892352	1021413	11.4864%
   reads: 	9034484	1083436	11.9922%
----------------
match_TE:2:
  reads:	RAL-287.noGEN.end	RAL-287.noGEN.end.TE	percent
uq reads:	8892352	158280	1.7800%
   reads: 	9034484	158917	1.7590%
----------------
Candidate insertion sites in file: RAL-287_insert.txt
  reads:	4875
  uqreads:	4867
  Number of Candidate sites:	4867

Level 1 collapse of insertion sites in file: RAL-287_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	280

Level 1 annotation file: RAL-287_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-287_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-287.noGEN.front	RAL-287.noGEN.front.gendel	percent
uq reads:	8892352	969177	10.8990%
   reads: 	9034484	1038791	11.4981%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-287.noGEN.end	RAL-287.noGEN.end.gendel	percent
uq reads:	8892352	1045094	11.7527%
   reads: 	9034484	1107685	12.2606%
----------------
Candidate breakpoint sites in file: RAL-287_depletion.xls
  reads:	9477
  uqreads:	9401
  Number of reads supporting candidate sites:	9401

Level 1 collapse of depletion sites in file: RAL-287_depletion_level1.xls
  Number of Level 1 collapsed sites:	577