Insertion Pipeline
Bowtie2_wholegenome:
  reads:	KN35_1-HE.fastq.uq.polyn	KN35_1-HE.filter	percent
uq reads:	51378796	2158989	4.2021%
   reads: 	59835085	2453057	4.0997%
----------------
virus_structural_rna_repbase_filter:
  reads:	KN35_1-HE.filter	KN35_1-HE.nostrna	percent
uq reads:	2158989	2133574	98.8228%
   reads: 	2453057	2405783	98.0729%
----------------
TE_filter:
  reads:	KN35_1-HE.nostrna	KN35_1-HE.noTE	percent
uq reads:	2133574	2122768	99.4935%
   reads: 	2405783	2386477	99.1975%
----------------
match_dm6_mask_gen:1:
  reads:	KN35_1-HE.noGEN.front	KN35_1-HE.noGEN.front.gen	percent
uq reads:	2122768	1052104	49.5628%
   reads: 	2386477	1150450	48.2070%
----------------
match_TE:2:
  reads:	KN35_1-HE.noGEN.front	KN35_1-HE.noGEN.front.TE	percent
uq reads:	2122768	103284	4.8655%
   reads: 	2386477	115382	4.8348%
----------------
match_dm6_mask_gen:1:
  reads:	KN35_1-HE.noGEN.end	KN35_1-HE.noGEN.end.gen	percent
uq reads:	2122768	1091991	51.4418%
   reads: 	2386477	1199970	50.2821%
----------------
match_TE:2:
  reads:	KN35_1-HE.noGEN.end	KN35_1-HE.noGEN.end.TE	percent
uq reads:	2122768	103024	4.8533%
   reads: 	2386477	114998	4.8187%
----------------
Candidate insertion sites in file: KN35_1-HE_insert.txt
  reads:	19729
  uqreads:	17852
  Number of Candidate sites:	17852

Level 1 collapse of insertion sites in file: KN35_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	597

Level 1 annotation file: KN35_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
KN35_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	KN35_1-HE.noGEN.front	KN35_1-HE.noGEN.front.gendel	percent
uq reads:	2122768	1052104	49.5628%
   reads: 	2386477	1150450	48.2070%
----------------
match_dm6_mask_gen_del:1:
  reads:	KN35_1-HE.noGEN.end	KN35_1-HE.noGEN.end.gendel	percent
uq reads:	2122768	1091991	51.4418%
   reads: 	2386477	1199970	50.2821%
----------------
Candidate breakpoint sites in file: KN35_1-HE_depletion.xls
  reads:	61910
  uqreads:	55630
  Number of reads supporting candidate sites:	55630

Level 1 collapse of depletion sites in file: KN35_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3578