Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RG6N_1-HE.fastq.uq.polyn	RG6N_1-HE.filter	percent
uq reads:	42331235	1664371	3.9318%
   reads: 	43379091	1731354	3.9912%
----------------
virus_structural_rna_repbase_filter:
  reads:	RG6N_1-HE.filter	RG6N_1-HE.nostrna	percent
uq reads:	1664371	1276603	76.7018%
   reads: 	1731354	1314177	75.9046%
----------------
TE_filter:
  reads:	RG6N_1-HE.nostrna	RG6N_1-HE.noTE	percent
uq reads:	1276603	1268822	99.3905%
   reads: 	1314177	1304936	99.2968%
----------------
match_dm6_mask_gen:1:
  reads:	RG6N_1-HE.noGEN.front	RG6N_1-HE.noGEN.front.gen	percent
uq reads:	1268822	665653	52.4623%
   reads: 	1304936	676325	51.8282%
----------------
match_TE:2:
  reads:	RG6N_1-HE.noGEN.front	RG6N_1-HE.noGEN.front.TE	percent
uq reads:	1268822	93568	7.3744%
   reads: 	1304936	95325	7.3050%
----------------
match_dm6_mask_gen:1:
  reads:	RG6N_1-HE.noGEN.end	RG6N_1-HE.noGEN.end.gen	percent
uq reads:	1268822	614363	48.4200%
   reads: 	1304936	625695	47.9483%
----------------
match_TE:2:
  reads:	RG6N_1-HE.noGEN.end	RG6N_1-HE.noGEN.end.TE	percent
uq reads:	1268822	90156	7.1055%
   reads: 	1304936	91830	7.0371%
----------------
Candidate insertion sites in file: RG6N_1-HE_insert.txt
  reads:	24622
  uqreads:	24088
  Number of Candidate sites:	24088

Level 1 collapse of insertion sites in file: RG6N_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	599

Level 1 annotation file: RG6N_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
RG6N_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RG6N_1-HE.noGEN.front	RG6N_1-HE.noGEN.front.gendel	percent
uq reads:	1268822	665653	52.4623%
   reads: 	1304936	676325	51.8282%
----------------
match_dm6_mask_gen_del:1:
  reads:	RG6N_1-HE.noGEN.end	RG6N_1-HE.noGEN.end.gendel	percent
uq reads:	1268822	614363	48.4200%
   reads: 	1304936	625695	47.9483%
----------------
Candidate breakpoint sites in file: RG6N_1-HE_depletion.xls
  reads:	95521
  uqreads:	93460
  Number of reads supporting candidate sites:	93460

Level 1 collapse of depletion sites in file: RG6N_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	5162