Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ZI273N-HE.fastq.uq.polyn	ZI273N-HE.filter	percent
uq reads:	40554714	2524640	6.2253%
   reads: 	41657247	2644261	6.3477%
----------------
virus_structural_rna_repbase_filter:
  reads:	ZI273N-HE.filter	ZI273N-HE.nostrna	percent
uq reads:	2524640	2206362	87.3931%
   reads: 	2644261	2283414	86.3536%
----------------
TE_filter:
  reads:	ZI273N-HE.nostrna	ZI273N-HE.noTE	percent
uq reads:	2206362	2200169	99.7193%
   reads: 	2283414	2276770	99.7090%
----------------
match_dm6_mask_gen:1:
  reads:	ZI273N-HE.noGEN.front	ZI273N-HE.noGEN.front.gen	percent
uq reads:	2200169	1149545	52.2480%
   reads: 	2276770	1171980	51.4756%
----------------
match_TE:2:
  reads:	ZI273N-HE.noGEN.front	ZI273N-HE.noGEN.front.TE	percent
uq reads:	2200169	165418	7.5184%
   reads: 	2276770	169384	7.4397%
----------------
match_dm6_mask_gen:1:
  reads:	ZI273N-HE.noGEN.end	ZI273N-HE.noGEN.end.gen	percent
uq reads:	2200169	1001913	45.5380%
   reads: 	2276770	1023322	44.9462%
----------------
match_TE:2:
  reads:	ZI273N-HE.noGEN.end	ZI273N-HE.noGEN.end.TE	percent
uq reads:	2200169	154194	7.0083%
   reads: 	2276770	158106	6.9443%
----------------
Candidate insertion sites in file: ZI273N-HE_insert.txt
  reads:	28214
  uqreads:	27714
  Number of Candidate sites:	27714

Level 1 collapse of insertion sites in file: ZI273N-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	575

Level 1 annotation file: ZI273N-HE_level1siteannotation.xls
Insertion sites in fixed bin:
ZI273N-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ZI273N-HE.noGEN.front	ZI273N-HE.noGEN.front.gendel	percent
uq reads:	2200169	1149545	52.2480%
   reads: 	2276770	1171980	51.4756%
----------------
match_dm6_mask_gen_del:1:
  reads:	ZI273N-HE.noGEN.end	ZI273N-HE.noGEN.end.gendel	percent
uq reads:	2200169	1001913	45.5380%
   reads: 	2276770	1023322	44.9462%
----------------
Candidate breakpoint sites in file: ZI273N-HE_depletion.xls
  reads:	195555
  uqreads:	191431
  Number of reads supporting candidate sites:	191431

Level 1 collapse of depletion sites in file: ZI273N-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	6534