Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ZI227-HE.fastq.uq.polyn	ZI227-HE.filter	percent
uq reads:	48759163	2454004	5.0329%
   reads: 	50778841	2634286	5.1878%
----------------
virus_structural_rna_repbase_filter:
  reads:	ZI227-HE.filter	ZI227-HE.nostrna	percent
uq reads:	2454004	1797547	73.2496%
   reads: 	2634286	1883620	71.5040%
----------------
TE_filter:
  reads:	ZI227-HE.nostrna	ZI227-HE.noTE	percent
uq reads:	1797547	1791971	99.6898%
   reads: 	1883620	1877424	99.6711%
----------------
match_dm6_mask_gen:1:
  reads:	ZI227-HE.noGEN.front	ZI227-HE.noGEN.front.gen	percent
uq reads:	1791971	959467	53.5426%
   reads: 	1877424	984798	52.4547%
----------------
match_TE:2:
  reads:	ZI227-HE.noGEN.front	ZI227-HE.noGEN.front.TE	percent
uq reads:	1791971	128384	7.1644%
   reads: 	1877424	131705	7.0152%
----------------
match_dm6_mask_gen:1:
  reads:	ZI227-HE.noGEN.end	ZI227-HE.noGEN.end.gen	percent
uq reads:	1791971	881803	49.2086%
   reads: 	1877424	908193	48.3744%
----------------
match_TE:2:
  reads:	ZI227-HE.noGEN.end	ZI227-HE.noGEN.end.TE	percent
uq reads:	1791971	123193	6.8747%
   reads: 	1877424	126419	6.7336%
----------------
Candidate insertion sites in file: ZI227-HE_insert.txt
  reads:	30341
  uqreads:	29312
  Number of Candidate sites:	29312

Level 1 collapse of insertion sites in file: ZI227-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	574

Level 1 annotation file: ZI227-HE_level1siteannotation.xls
Insertion sites in fixed bin:
ZI227-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ZI227-HE.noGEN.front	ZI227-HE.noGEN.front.gendel	percent
uq reads:	1791971	959467	53.5426%
   reads: 	1877424	984798	52.4547%
----------------
match_dm6_mask_gen_del:1:
  reads:	ZI227-HE.noGEN.end	ZI227-HE.noGEN.end.gendel	percent
uq reads:	1791971	881803	49.2086%
   reads: 	1877424	908193	48.3744%
----------------
Candidate breakpoint sites in file: ZI227-HE_depletion.xls
  reads:	125668
  uqreads:	120995
  Number of reads supporting candidate sites:	120995

Level 1 collapse of depletion sites in file: ZI227-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	5461