Insertion Pipeline
Bowtie2_wholegenome:
  reads:	CanS-BS.fastq.uq.polyn	CanS-BS.filter	percent
uq reads:	41565827	10170560	24.4686%
   reads: 	56528271	11675602	20.6544%
----------------
virus_structural_rna_repbase_filter:
  reads:	CanS-BS.filter	CanS-BS.nostrna	percent
uq reads:	10170560	10139467	99.6943%
   reads: 	11675602	11537503	98.8172%
----------------
TE_filter:
  reads:	CanS-BS.nostrna	CanS-BS.noTE	percent
uq reads:	10139467	10130879	99.9153%
   reads: 	11537503	11515620	99.8103%
----------------
match_dm6_mask_gen:1:
  reads:	CanS-BS.noGEN.front	CanS-BS.noGEN.front.gen	percent
uq reads:	10130879	7185801	70.9297%
   reads: 	11515620	7597792	65.9781%
----------------
match_TE:2:
  reads:	CanS-BS.noGEN.front	CanS-BS.noGEN.front.TE	percent
uq reads:	10130879	862463	8.5132%
   reads: 	11515620	960887	8.3442%
----------------
match_dm6_mask_gen:1:
  reads:	CanS-BS.noGEN.end	CanS-BS.noGEN.end.gen	percent
uq reads:	10130879	230359	2.2738%
   reads: 	11515620	345409	2.9995%
----------------
match_TE:2:
  reads:	CanS-BS.noGEN.end	CanS-BS.noGEN.end.TE	percent
uq reads:	10130879	40738	0.4021%
   reads: 	11515620	59175	0.5139%
----------------
Candidate insertion sites in file: CanS-BS_insert.txt
  reads:	15106
  uqreads:	11508
  Number of Candidate sites:	11508

Level 1 collapse of insertion sites in file: CanS-BS_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	677

Level 1 annotation file: CanS-BS_level1siteannotation.xls
Insertion sites in fixed bin:
CanS-BS_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	CanS-BS.noGEN.front	CanS-BS.noGEN.front.gendel	percent
uq reads:	10130879	7185801	70.9297%
   reads: 	11515620	7597792	65.9781%
----------------
match_dm6_mask_gen_del:1:
  reads:	CanS-BS.noGEN.end	CanS-BS.noGEN.end.gendel	percent
uq reads:	10130879	230359	2.2738%
   reads: 	11515620	345409	2.9995%
----------------
Candidate breakpoint sites in file: CanS-BS_depletion.xls
  reads:	38165
  uqreads:	28060
  Number of reads supporting candidate sites:	28060

Level 1 collapse of depletion sites in file: CanS-BS_depletion_level1.xls
  Number of Level 1 collapsed sites:	2717