Insertion Pipeline
Bowtie2_wholegenome:
  reads:	SB31_1-HE.fastq.uq.polyn	SB31_1-HE.filter	percent
uq reads:	39552983	3036723	7.6776%
   reads: 	42506347	3100321	7.2938%
----------------
virus_structural_rna_repbase_filter:
  reads:	SB31_1-HE.filter	SB31_1-HE.nostrna	percent
uq reads:	3036723	2857993	94.1144%
   reads: 	3100321	2911449	93.9080%
----------------
TE_filter:
  reads:	SB31_1-HE.nostrna	SB31_1-HE.noTE	percent
uq reads:	2857993	2853787	99.8528%
   reads: 	2911449	2906106	99.8165%
----------------
match_dm6_mask_gen:1:
  reads:	SB31_1-HE.noGEN.front	SB31_1-HE.noGEN.front.gen	percent
uq reads:	2853787	1811517	63.4777%
   reads: 	2906106	1833409	63.0882%
----------------
match_TE:2:
  reads:	SB31_1-HE.noGEN.front	SB31_1-HE.noGEN.front.TE	percent
uq reads:	2853787	190594	6.6786%
   reads: 	2906106	195492	6.7269%
----------------
match_dm6_mask_gen:1:
  reads:	SB31_1-HE.noGEN.end	SB31_1-HE.noGEN.end.gen	percent
uq reads:	2853787	1547902	54.2403%
   reads: 	2906106	1570412	54.0384%
----------------
match_TE:2:
  reads:	SB31_1-HE.noGEN.end	SB31_1-HE.noGEN.end.TE	percent
uq reads:	2853787	170830	5.9861%
   reads: 	2906106	175922	6.0535%
----------------
Candidate insertion sites in file: SB31_1-HE_insert.txt
  reads:	31032
  uqreads:	30434
  Number of Candidate sites:	30434

Level 1 collapse of insertion sites in file: SB31_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	451

Level 1 annotation file: SB31_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
SB31_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	SB31_1-HE.noGEN.front	SB31_1-HE.noGEN.front.gendel	percent
uq reads:	2853787	1811517	63.4777%
   reads: 	2906106	1833409	63.0882%
----------------
match_dm6_mask_gen_del:1:
  reads:	SB31_1-HE.noGEN.end	SB31_1-HE.noGEN.end.gendel	percent
uq reads:	2853787	1547902	54.2403%
   reads: 	2906106	1570412	54.0384%
----------------
Candidate breakpoint sites in file: SB31_1-HE_depletion.xls
  reads:	118288
  uqreads:	115730
  Number of reads supporting candidate sites:	115730

Level 1 collapse of depletion sites in file: SB31_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3081