Insertion Pipeline
Bowtie2_wholegenome:
  reads:	NG6N_1-HE.fastq.uq.polyn	NG6N_1-HE.filter	percent
uq reads:	58253433	2647212	4.5443%
   reads: 	67063906	3023118	4.5078%
----------------
virus_structural_rna_repbase_filter:
  reads:	NG6N_1-HE.filter	NG6N_1-HE.nostrna	percent
uq reads:	2647212	1922418	72.6205%
   reads: 	3023118	2140328	70.7987%
----------------
TE_filter:
  reads:	NG6N_1-HE.nostrna	NG6N_1-HE.noTE	percent
uq reads:	1922418	1913435	99.5327%
   reads: 	2140328	2124066	99.2402%
----------------
match_dm6_mask_gen:1:
  reads:	NG6N_1-HE.noGEN.front	NG6N_1-HE.noGEN.front.gen	percent
uq reads:	1913435	941471	49.2032%
   reads: 	2124066	1020567	48.0478%
----------------
match_TE:2:
  reads:	NG6N_1-HE.noGEN.front	NG6N_1-HE.noGEN.front.TE	percent
uq reads:	1913435	82222	4.2971%
   reads: 	2124066	89952	4.2349%
----------------
match_dm6_mask_gen:1:
  reads:	NG6N_1-HE.noGEN.end	NG6N_1-HE.noGEN.end.gen	percent
uq reads:	1913435	951581	49.7316%
   reads: 	2124066	1038560	48.8949%
----------------
match_TE:2:
  reads:	NG6N_1-HE.noGEN.end	NG6N_1-HE.noGEN.end.TE	percent
uq reads:	1913435	80820	4.2238%
   reads: 	2124066	88375	4.1607%
----------------
Candidate insertion sites in file: NG6N_1-HE_insert.txt
  reads:	20066
  uqreads:	18149
  Number of Candidate sites:	18149

Level 1 collapse of insertion sites in file: NG6N_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	620

Level 1 annotation file: NG6N_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
NG6N_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	NG6N_1-HE.noGEN.front	NG6N_1-HE.noGEN.front.gendel	percent
uq reads:	1913435	941471	49.2032%
   reads: 	2124066	1020567	48.0478%
----------------
match_dm6_mask_gen_del:1:
  reads:	NG6N_1-HE.noGEN.end	NG6N_1-HE.noGEN.end.gendel	percent
uq reads:	1913435	951581	49.7316%
   reads: 	2124066	1038560	48.8949%
----------------
Candidate breakpoint sites in file: NG6N_1-HE_depletion.xls
  reads:	57207
  uqreads:	51592
  Number of reads supporting candidate sites:	51592

Level 1 collapse of depletion sites in file: NG6N_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3140