Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RG4N_1-HE.fastq.uq.polyn	RG4N_1-HE.filter	percent
uq reads:	47314355	2734470	5.7794%
   reads: 	49022210	2816682	5.7457%
----------------
virus_structural_rna_repbase_filter:
  reads:	RG4N_1-HE.filter	RG4N_1-HE.nostrna	percent
uq reads:	2734470	2394357	87.5620%
   reads: 	2816682	2447073	86.8779%
----------------
TE_filter:
  reads:	RG4N_1-HE.nostrna	RG4N_1-HE.noTE	percent
uq reads:	2394357	2384938	99.6066%
   reads: 	2447073	2436047	99.5494%
----------------
match_dm6_mask_gen:1:
  reads:	RG4N_1-HE.noGEN.front	RG4N_1-HE.noGEN.front.gen	percent
uq reads:	2384938	1504971	63.1031%
   reads: 	2436047	1524022	62.5613%
----------------
match_TE:2:
  reads:	RG4N_1-HE.noGEN.front	RG4N_1-HE.noGEN.front.TE	percent
uq reads:	2384938	166937	6.9996%
   reads: 	2436047	169593	6.9618%
----------------
match_dm6_mask_gen:1:
  reads:	RG4N_1-HE.noGEN.end	RG4N_1-HE.noGEN.end.gen	percent
uq reads:	2384938	755327	31.6707%
   reads: 	2436047	774852	31.8078%
----------------
match_TE:2:
  reads:	RG4N_1-HE.noGEN.end	RG4N_1-HE.noGEN.end.TE	percent
uq reads:	2384938	99233	4.1608%
   reads: 	2436047	101804	4.1791%
----------------
Candidate insertion sites in file: RG4N_1-HE_insert.txt
  reads:	27174
  uqreads:	26387
  Number of Candidate sites:	26387

Level 1 collapse of insertion sites in file: RG4N_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	546

Level 1 annotation file: RG4N_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
RG4N_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RG4N_1-HE.noGEN.front	RG4N_1-HE.noGEN.front.gendel	percent
uq reads:	2384938	1504971	63.1031%
   reads: 	2436047	1524022	62.5613%
----------------
match_dm6_mask_gen_del:1:
  reads:	RG4N_1-HE.noGEN.end	RG4N_1-HE.noGEN.end.gendel	percent
uq reads:	2384938	755327	31.6707%
   reads: 	2436047	774852	31.8078%
----------------
Candidate breakpoint sites in file: RG4N_1-HE_depletion.xls
  reads:	113233
  uqreads:	109515
  Number of reads supporting candidate sites:	109515

Level 1 collapse of depletion sites in file: RG4N_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	5271