Insertion Pipeline
Bowtie2_wholegenome:
  reads:	KN20N_1-HE.fastq.uq.polyn	KN20N_1-HE.filter	percent
uq reads:	56020475	2269486	4.0512%
   reads: 	63336969	2507051	3.9583%
----------------
virus_structural_rna_repbase_filter:
  reads:	KN20N_1-HE.filter	KN20N_1-HE.nostrna	percent
uq reads:	2269486	2152290	94.8360%
   reads: 	2507051	2383890	95.0874%
----------------
TE_filter:
  reads:	KN20N_1-HE.nostrna	KN20N_1-HE.noTE	percent
uq reads:	2152290	2142267	99.5343%
   reads: 	2383890	2367389	99.3078%
----------------
match_dm6_mask_gen:1:
  reads:	KN20N_1-HE.noGEN.front	KN20N_1-HE.noGEN.front.gen	percent
uq reads:	2142267	1053992	49.1998%
   reads: 	2367389	1142461	48.2583%
----------------
match_TE:2:
  reads:	KN20N_1-HE.noGEN.front	KN20N_1-HE.noGEN.front.TE	percent
uq reads:	2142267	82039	3.8295%
   reads: 	2367389	89132	3.7650%
----------------
match_dm6_mask_gen:1:
  reads:	KN20N_1-HE.noGEN.end	KN20N_1-HE.noGEN.end.gen	percent
uq reads:	2142267	1082608	50.5356%
   reads: 	2367389	1181573	49.9104%
----------------
match_TE:2:
  reads:	KN20N_1-HE.noGEN.end	KN20N_1-HE.noGEN.end.TE	percent
uq reads:	2142267	80128	3.7403%
   reads: 	2367389	86848	3.6685%
----------------
Candidate insertion sites in file: KN20N_1-HE_insert.txt
  reads:	16728
  uqreads:	15175
  Number of Candidate sites:	15175

Level 1 collapse of insertion sites in file: KN20N_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	539

Level 1 annotation file: KN20N_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
KN20N_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	KN20N_1-HE.noGEN.front	KN20N_1-HE.noGEN.front.gendel	percent
uq reads:	2142267	1053992	49.1998%
   reads: 	2367389	1142461	48.2583%
----------------
match_dm6_mask_gen_del:1:
  reads:	KN20N_1-HE.noGEN.end	KN20N_1-HE.noGEN.end.gendel	percent
uq reads:	2142267	1082608	50.5356%
   reads: 	2367389	1181573	49.9104%
----------------
Candidate breakpoint sites in file: KN20N_1-HE_depletion.xls
  reads:	69095
  uqreads:	62723
  Number of reads supporting candidate sites:	62723

Level 1 collapse of depletion sites in file: KN20N_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3629