Insertion Pipeline
Bowtie2_wholegenome:
  reads:	CanS-TP.fastq.uq.polyn	CanS-TP.filter	percent
uq reads:	53647439	14221043	26.5083%
   reads: 	75076206	16065479	21.3989%
----------------
virus_structural_rna_repbase_filter:
  reads:	CanS-TP.filter	CanS-TP.nostrna	percent
uq reads:	14221043	14188202	99.7691%
   reads: 	16065479	15882961	98.8639%
----------------
TE_filter:
  reads:	CanS-TP.nostrna	CanS-TP.noTE	percent
uq reads:	14188202	14186805	99.9902%
   reads: 	15882961	15880972	99.9875%
----------------
match_dm6_mask_gen:1:
  reads:	CanS-TP.noGEN.front	CanS-TP.noGEN.front.gen	percent
uq reads:	14186805	10648711	75.0607%
   reads: 	15880972	11258425	70.8925%
----------------
match_TE:2:
  reads:	CanS-TP.noGEN.front	CanS-TP.noGEN.front.TE	percent
uq reads:	14186805	1196797	8.4360%
   reads: 	15880972	1371956	8.6390%
----------------
match_dm6_mask_gen:1:
  reads:	CanS-TP.noGEN.end	CanS-TP.noGEN.end.gen	percent
uq reads:	14186805	262548	1.8506%
   reads: 	15880972	416497	2.6226%
----------------
match_TE:2:
  reads:	CanS-TP.noGEN.end	CanS-TP.noGEN.end.TE	percent
uq reads:	14186805	49141	0.3464%
   reads: 	15880972	72315	0.4554%
----------------
Candidate insertion sites in file: CanS-TP_insert.txt
  reads:	17912
  uqreads:	12781
  Number of Candidate sites:	12781

Level 1 collapse of insertion sites in file: CanS-TP_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	636

Level 1 annotation file: CanS-TP_level1siteannotation.xls
Insertion sites in fixed bin:
CanS-TP_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	CanS-TP.noGEN.front	CanS-TP.noGEN.front.gendel	percent
uq reads:	14186805	10648711	75.0607%
   reads: 	15880972	11258425	70.8925%
----------------
match_dm6_mask_gen_del:1:
  reads:	CanS-TP.noGEN.end	CanS-TP.noGEN.end.gendel	percent
uq reads:	14186805	262548	1.8506%
   reads: 	15880972	416497	2.6226%
----------------
Candidate breakpoint sites in file: CanS-TP_depletion.xls
  reads:	46822
  uqreads:	32409
  Number of reads supporting candidate sites:	32409

Level 1 collapse of depletion sites in file: CanS-TP_depletion_level1.xls
  Number of Level 1 collapsed sites:	2728