Insertion Pipeline
Bowtie2_wholegenome:
  reads:	D17-c3.fastq.uq.polyn	D17-c3.filter	percent
uq reads:	69205070	2367657	3.4212%
   reads: 	86264154	5199759	6.0277%
----------------
virus_structural_rna_repbase_filter:
  reads:	D17-c3.filter	D17-c3.nostrna	percent
uq reads:	2367657	2345339	99.0574%
   reads: 	5199759	5159884	99.2331%
----------------
TE_filter:
  reads:	D17-c3.nostrna	D17-c3.noTE	percent
uq reads:	2345339	2334627	99.5433%
   reads: 	5159884	5147349	99.7571%
----------------
match_dm6_mask_gen:1:
  reads:	D17-c3.noGEN.front	D17-c3.noGEN.front.gen	percent
uq reads:	2334627	644712	27.6152%
   reads: 	5147349	1516365	29.4591%
----------------
match_TE:2:
  reads:	D17-c3.noGEN.front	D17-c3.noGEN.front.TE	percent
uq reads:	2334627	158864	6.8047%
   reads: 	5147349	187149	3.6358%
----------------
match_dm6_mask_gen:1:
  reads:	D17-c3.noGEN.end	D17-c3.noGEN.end.gen	percent
uq reads:	2334627	555952	23.8133%
   reads: 	5147349	1452411	28.2167%
----------------
match_TE:2:
  reads:	D17-c3.noGEN.end	D17-c3.noGEN.end.TE	percent
uq reads:	2334627	148660	6.3676%
   reads: 	5147349	177991	3.4579%
----------------
Candidate insertion sites in file: D17-c3_insert.txt
  reads:	50698
  uqreads:	46739
  Number of Candidate sites:	46739

Level 1 collapse of insertion sites in file: D17-c3_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1977

Level 1 annotation file: D17-c3_level1siteannotation.xls
Insertion sites in fixed bin:
D17-c3_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	D17-c3.noGEN.front	D17-c3.noGEN.front.gendel	percent
uq reads:	2334627	644712	27.6152%
   reads: 	5147349	1516365	29.4591%
----------------
match_dm6_mask_gen_del:1:
  reads:	D17-c3.noGEN.end	D17-c3.noGEN.end.gendel	percent
uq reads:	2334627	555952	23.8133%
   reads: 	5147349	1452411	28.2167%
----------------
Candidate breakpoint sites in file: D17-c3_depletion.xls
  reads:	63943
  uqreads:	56721
  Number of reads supporting candidate sites:	56721

Level 1 collapse of depletion sites in file: D17-c3_depletion_level1.xls
  Number of Level 1 collapsed sites:	3412