Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-28.fastq.uq.polyn	RAL-28.filter	percent
uq reads:	25160954	1759248	6.9920%
   reads: 	26247075	1953668	7.4434%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-28.filter	RAL-28.nostrna	percent
uq reads:	1759248	1722123	97.8897%
   reads: 	1953668	1912166	97.8757%
----------------
TE_filter:
  reads:	RAL-28.nostrna	RAL-28.noTE	percent
uq reads:	1722123	1715482	99.6144%
   reads: 	1912166	1904961	99.6232%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-28.noGEN.front	RAL-28.noGEN.front.gen	percent
uq reads:	1715482	428570	24.9825%
   reads: 	1904961	544988	28.6089%
----------------
match_TE:2:
  reads:	RAL-28.noGEN.front	RAL-28.noGEN.front.TE	percent
uq reads:	1715482	56283	3.2809%
   reads: 	1904961	58845	3.0890%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-28.noGEN.end	RAL-28.noGEN.end.gen	percent
uq reads:	1715482	351085	20.4657%
   reads: 	1904961	467558	24.5442%
----------------
match_TE:2:
  reads:	RAL-28.noGEN.end	RAL-28.noGEN.end.TE	percent
uq reads:	1715482	51214	2.9854%
   reads: 	1904961	53830	2.8258%
----------------
Candidate insertion sites in file: RAL-28_insert.txt
  reads:	5317
  uqreads:	5260
  Number of Candidate sites:	5260

Level 1 collapse of insertion sites in file: RAL-28_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	405

Level 1 annotation file: RAL-28_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-28_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-28.noGEN.front	RAL-28.noGEN.front.gendel	percent
uq reads:	1715482	428570	24.9825%
   reads: 	1904961	544988	28.6089%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-28.noGEN.end	RAL-28.noGEN.end.gendel	percent
uq reads:	1715482	351085	20.4657%
   reads: 	1904961	467558	24.5442%
----------------
Candidate breakpoint sites in file: RAL-28_depletion.xls
  reads:	12557
  uqreads:	12305
  Number of reads supporting candidate sites:	12305

Level 1 collapse of depletion sites in file: RAL-28_depletion_level1.xls
  Number of Level 1 collapsed sites:	1252