Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-227.fastq.uq.polyn	RAL-227.filter	percent
uq reads:	28344245	3611249	12.7407%
   reads: 	30678403	4229047	13.7851%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-227.filter	RAL-227.nostrna	percent
uq reads:	3611249	2155310	59.6832%
   reads: 	4229047	2454721	58.0443%
----------------
TE_filter:
  reads:	RAL-227.nostrna	RAL-227.noTE	percent
uq reads:	2155310	2140570	99.3161%
   reads: 	2454721	2436033	99.2387%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-227.noGEN.front	RAL-227.noGEN.front.gen	percent
uq reads:	2140570	574687	26.8474%
   reads: 	2436033	712356	29.2425%
----------------
match_TE:2:
  reads:	RAL-227.noGEN.front	RAL-227.noGEN.front.TE	percent
uq reads:	2140570	83614	3.9062%
   reads: 	2436033	89790	3.6859%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-227.noGEN.end	RAL-227.noGEN.end.gen	percent
uq reads:	2140570	465510	21.7470%
   reads: 	2436033	596174	24.4731%
----------------
match_TE:2:
  reads:	RAL-227.noGEN.end	RAL-227.noGEN.end.TE	percent
uq reads:	2140570	75514	3.5278%
   reads: 	2436033	82286	3.3779%
----------------
Candidate insertion sites in file: RAL-227_insert.txt
  reads:	8239
  uqreads:	8090
  Number of Candidate sites:	8090

Level 1 collapse of insertion sites in file: RAL-227_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	587

Level 1 annotation file: RAL-227_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-227_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-227.noGEN.front	RAL-227.noGEN.front.gendel	percent
uq reads:	2140570	574687	26.8474%
   reads: 	2436033	712356	29.2425%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-227.noGEN.end	RAL-227.noGEN.end.gendel	percent
uq reads:	2140570	465510	21.7470%
   reads: 	2436033	596174	24.4731%
----------------
Candidate breakpoint sites in file: RAL-227_depletion.xls
  reads:	15282
  uqreads:	14911
  Number of reads supporting candidate sites:	14911

Level 1 collapse of depletion sites in file: RAL-227_depletion_level1.xls
  Number of Level 1 collapsed sites:	1546