Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-712.fastq.uq.polyn	RAL-712.filter	percent
uq reads:	40639130	8000320	19.6862%
   reads: 	43515424	8914069	20.4848%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-712.filter	RAL-712.nostrna	percent
uq reads:	8000320	6060048	75.7476%
   reads: 	8914069	6541425	73.3832%
----------------
TE_filter:
  reads:	RAL-712.nostrna	RAL-712.noTE	percent
uq reads:	6060048	6051875	99.8651%
   reads: 	6541425	6531787	99.8527%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-712.noGEN.front	RAL-712.noGEN.front.gen	percent
uq reads:	6051875	1916710	31.6713%
   reads: 	6531787	2196536	33.6284%
----------------
match_TE:2:
  reads:	RAL-712.noGEN.front	RAL-712.noGEN.front.TE	percent
uq reads:	6051875	296465	4.8987%
   reads: 	6531787	302046	4.6242%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-712.noGEN.end	RAL-712.noGEN.end.gen	percent
uq reads:	6051875	538649	8.9005%
   reads: 	6531787	796053	12.1874%
----------------
match_TE:2:
  reads:	RAL-712.noGEN.end	RAL-712.noGEN.end.TE	percent
uq reads:	6051875	132007	2.1813%
   reads: 	6531787	139260	2.1320%
----------------
Candidate insertion sites in file: RAL-712_insert.txt
  reads:	9300
  uqreads:	9084
  Number of Candidate sites:	9084

Level 1 collapse of insertion sites in file: RAL-712_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	427

Level 1 annotation file: RAL-712_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-712_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-712.noGEN.front	RAL-712.noGEN.front.gendel	percent
uq reads:	6051875	1916710	31.6713%
   reads: 	6531787	2196536	33.6284%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-712.noGEN.end	RAL-712.noGEN.end.gendel	percent
uq reads:	6051875	538649	8.9005%
   reads: 	6531787	796053	12.1874%
----------------
Candidate breakpoint sites in file: RAL-712_depletion.xls
  reads:	19953
  uqreads:	18666
  Number of reads supporting candidate sites:	18666

Level 1 collapse of depletion sites in file: RAL-712_depletion_level1.xls
  Number of Level 1 collapsed sites:	1896