Insertion Pipeline
Bowtie2_wholegenome:
  reads:	KT6_1-HE.fastq.uq.polyn	KT6_1-HE.filter	percent
uq reads:	47608075	2097613	4.4060%
   reads: 	53800883	2310281	4.2941%
----------------
virus_structural_rna_repbase_filter:
  reads:	KT6_1-HE.filter	KT6_1-HE.nostrna	percent
uq reads:	2097613	1642326	78.2950%
   reads: 	2310281	1796280	77.7516%
----------------
TE_filter:
  reads:	KT6_1-HE.nostrna	KT6_1-HE.noTE	percent
uq reads:	1642326	1636065	99.6188%
   reads: 	1796280	1784456	99.3418%
----------------
match_dm6_mask_gen:1:
  reads:	KT6_1-HE.noGEN.front	KT6_1-HE.noGEN.front.gen	percent
uq reads:	1636065	744234	45.4893%
   reads: 	1784456	796965	44.6615%
----------------
match_TE:2:
  reads:	KT6_1-HE.noGEN.front	KT6_1-HE.noGEN.front.TE	percent
uq reads:	1636065	83627	5.1115%
   reads: 	1784456	91928	5.1516%
----------------
match_dm6_mask_gen:1:
  reads:	KT6_1-HE.noGEN.end	KT6_1-HE.noGEN.end.gen	percent
uq reads:	1636065	806150	49.2737%
   reads: 	1784456	865324	48.4923%
----------------
match_TE:2:
  reads:	KT6_1-HE.noGEN.end	KT6_1-HE.noGEN.end.TE	percent
uq reads:	1636065	86558	5.2906%
   reads: 	1784456	94881	5.3171%
----------------
Candidate insertion sites in file: KT6_1-HE_insert.txt
  reads:	14653
  uqreads:	13496
  Number of Candidate sites:	13496

Level 1 collapse of insertion sites in file: KT6_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	560

Level 1 annotation file: KT6_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
KT6_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	KT6_1-HE.noGEN.front	KT6_1-HE.noGEN.front.gendel	percent
uq reads:	1636065	744234	45.4893%
   reads: 	1784456	796965	44.6615%
----------------
match_dm6_mask_gen_del:1:
  reads:	KT6_1-HE.noGEN.end	KT6_1-HE.noGEN.end.gendel	percent
uq reads:	1636065	806150	49.2737%
   reads: 	1784456	865324	48.4923%
----------------
Candidate breakpoint sites in file: KT6_1-HE_depletion.xls
  reads:	44926
  uqreads:	41060
  Number of reads supporting candidate sites:	41060

Level 1 collapse of depletion sites in file: KT6_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3136