Insertion Pipeline
Bowtie2_wholegenome:
  reads:	CanS-TZ.fastq.uq.polyn	CanS-TZ.filter	percent
uq reads:	56480917	14506830	25.6845%
   reads: 	79851405	16432790	20.5792%
----------------
virus_structural_rna_repbase_filter:
  reads:	CanS-TZ.filter	CanS-TZ.nostrna	percent
uq reads:	14506830	14473581	99.7708%
   reads: 	16432790	16248641	98.8794%
----------------
TE_filter:
  reads:	CanS-TZ.nostrna	CanS-TZ.noTE	percent
uq reads:	14473581	14471772	99.9875%
   reads: 	16248641	16246098	99.9843%
----------------
match_dm6_mask_gen:1:
  reads:	CanS-TZ.noGEN.front	CanS-TZ.noGEN.front.gen	percent
uq reads:	14471772	10699139	73.9311%
   reads: 	16246098	11282182	69.4455%
----------------
match_TE:2:
  reads:	CanS-TZ.noGEN.front	CanS-TZ.noGEN.front.TE	percent
uq reads:	14471772	1191155	8.2309%
   reads: 	16246098	1354302	8.3362%
----------------
match_dm6_mask_gen:1:
  reads:	CanS-TZ.noGEN.end	CanS-TZ.noGEN.end.gen	percent
uq reads:	14471772	293680	2.0293%
   reads: 	16246098	467177	2.8756%
----------------
match_TE:2:
  reads:	CanS-TZ.noGEN.end	CanS-TZ.noGEN.end.TE	percent
uq reads:	14471772	53333	0.3685%
   reads: 	16246098	78951	0.4860%
----------------
Candidate insertion sites in file: CanS-TZ_insert.txt
  reads:	19755
  uqreads:	14201
  Number of Candidate sites:	14201

Level 1 collapse of insertion sites in file: CanS-TZ_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	747

Level 1 annotation file: CanS-TZ_level1siteannotation.xls
Insertion sites in fixed bin:
CanS-TZ_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	CanS-TZ.noGEN.front	CanS-TZ.noGEN.front.gendel	percent
uq reads:	14471772	10699139	73.9311%
   reads: 	16246098	11282182	69.4455%
----------------
match_dm6_mask_gen_del:1:
  reads:	CanS-TZ.noGEN.end	CanS-TZ.noGEN.end.gendel	percent
uq reads:	14471772	293680	2.0293%
   reads: 	16246098	467177	2.8756%
----------------
Candidate breakpoint sites in file: CanS-TZ_depletion.xls
  reads:	52708
  uqreads:	36031
  Number of reads supporting candidate sites:	36031

Level 1 collapse of depletion sites in file: CanS-TZ_depletion_level1.xls
  Number of Level 1 collapsed sites:	2981