Insertion Pipeline
Bowtie2_wholegenome:
  reads:	CanS-HS.fastq.uq.polyn	CanS-HS.filter	percent
uq reads:	60007990	20545417	34.2378%
   reads: 	81261885	23750933	29.2276%
----------------
virus_structural_rna_repbase_filter:
  reads:	CanS-HS.filter	CanS-HS.nostrna	percent
uq reads:	20545417	19983201	97.2635%
   reads: 	23750933	22543623	94.9168%
----------------
TE_filter:
  reads:	CanS-HS.nostrna	CanS-HS.noTE	percent
uq reads:	19983201	19980532	99.9866%
   reads: 	22543623	22539148	99.9801%
----------------
match_dm6_mask_gen:1:
  reads:	CanS-HS.noGEN.front	CanS-HS.noGEN.front.gen	percent
uq reads:	19980532	14495155	72.5464%
   reads: 	22539148	15291519	67.8443%
----------------
match_TE:2:
  reads:	CanS-HS.noGEN.front	CanS-HS.noGEN.front.TE	percent
uq reads:	19980532	1725944	8.6381%
   reads: 	22539148	1995235	8.8523%
----------------
match_dm6_mask_gen:1:
  reads:	CanS-HS.noGEN.end	CanS-HS.noGEN.end.gen	percent
uq reads:	19980532	271250	1.3576%
   reads: 	22539148	433324	1.9225%
----------------
match_TE:2:
  reads:	CanS-HS.noGEN.end	CanS-HS.noGEN.end.TE	percent
uq reads:	19980532	51503	0.2578%
   reads: 	22539148	78539	0.3485%
----------------
Candidate insertion sites in file: CanS-HS_insert.txt
  reads:	19047
  uqreads:	13861
  Number of Candidate sites:	13861

Level 1 collapse of insertion sites in file: CanS-HS_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	725

Level 1 annotation file: CanS-HS_level1siteannotation.xls
Insertion sites in fixed bin:
CanS-HS_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	CanS-HS.noGEN.front	CanS-HS.noGEN.front.gendel	percent
uq reads:	19980532	14495155	72.5464%
   reads: 	22539148	15291519	67.8443%
----------------
match_dm6_mask_gen_del:1:
  reads:	CanS-HS.noGEN.end	CanS-HS.noGEN.end.gendel	percent
uq reads:	19980532	271250	1.3576%
   reads: 	22539148	433324	1.9225%
----------------
Candidate breakpoint sites in file: CanS-HS_depletion.xls
  reads:	48943
  uqreads:	34612
  Number of reads supporting candidate sites:	34612

Level 1 collapse of depletion sites in file: CanS-HS_depletion_level1.xls
  Number of Level 1 collapsed sites:	2969