Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ZI191-HE.fastq.uq.polyn	ZI191-HE.filter	percent
uq reads:	43141759	2216791	5.1384%
   reads: 	45849701	2383185	5.1978%
----------------
virus_structural_rna_repbase_filter:
  reads:	ZI191-HE.filter	ZI191-HE.nostrna	percent
uq reads:	2216791	2114473	95.3844%
   reads: 	2383185	2246290	94.2558%
----------------
TE_filter:
  reads:	ZI191-HE.nostrna	ZI191-HE.noTE	percent
uq reads:	2114473	2101877	99.4043%
   reads: 	2246290	2228403	99.2037%
----------------
match_dm6_mask_gen:1:
  reads:	ZI191-HE.noGEN.front	ZI191-HE.noGEN.front.gen	percent
uq reads:	2101877	1151295	54.7746%
   reads: 	2228403	1203994	54.0295%
----------------
match_TE:2:
  reads:	ZI191-HE.noGEN.front	ZI191-HE.noGEN.front.TE	percent
uq reads:	2101877	126291	6.0085%
   reads: 	2228403	131303	5.8922%
----------------
match_dm6_mask_gen:1:
  reads:	ZI191-HE.noGEN.end	ZI191-HE.noGEN.end.gen	percent
uq reads:	2101877	982035	46.7218%
   reads: 	2228403	1033006	46.3563%
----------------
match_TE:2:
  reads:	ZI191-HE.noGEN.end	ZI191-HE.noGEN.end.TE	percent
uq reads:	2101877	114334	5.4396%
   reads: 	2228403	119059	5.3428%
----------------
Candidate insertion sites in file: ZI191-HE_insert.txt
  reads:	29417
  uqreads:	27964
  Number of Candidate sites:	27964

Level 1 collapse of insertion sites in file: ZI191-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	546

Level 1 annotation file: ZI191-HE_level1siteannotation.xls
Insertion sites in fixed bin:
ZI191-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ZI191-HE.noGEN.front	ZI191-HE.noGEN.front.gendel	percent
uq reads:	2101877	1151295	54.7746%
   reads: 	2228403	1203994	54.0295%
----------------
match_dm6_mask_gen_del:1:
  reads:	ZI191-HE.noGEN.end	ZI191-HE.noGEN.end.gendel	percent
uq reads:	2101877	982035	46.7218%
   reads: 	2228403	1033006	46.3563%
----------------
Candidate breakpoint sites in file: ZI191-HE_depletion.xls
  reads:	130190
  uqreads:	122280
  Number of reads supporting candidate sites:	122280

Level 1 collapse of depletion sites in file: ZI191-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	5587