Insertion Pipeline
Bowtie2_wholegenome:
  reads:	GA130_1-HE.fastq.uq.polyn	GA130_1-HE.filter	percent
uq reads:	70321463	2230708	3.1722%
   reads: 	85862995	2546714	2.9660%
----------------
virus_structural_rna_repbase_filter:
  reads:	GA130_1-HE.filter	GA130_1-HE.nostrna	percent
uq reads:	2230708	2197331	98.5037%
   reads: 	2546714	2493922	97.9271%
----------------
TE_filter:
  reads:	GA130_1-HE.nostrna	GA130_1-HE.noTE	percent
uq reads:	2197331	2186896	99.5251%
   reads: 	2493922	2478728	99.3908%
----------------
match_dm6_mask_gen:1:
  reads:	GA130_1-HE.noGEN.front	GA130_1-HE.noGEN.front.gen	percent
uq reads:	2186896	1075790	49.1926%
   reads: 	2478728	1185361	47.8213%
----------------
match_TE:2:
  reads:	GA130_1-HE.noGEN.front	GA130_1-HE.noGEN.front.TE	percent
uq reads:	2186896	135485	6.1953%
   reads: 	2478728	152507	6.1526%
----------------
match_dm6_mask_gen:1:
  reads:	GA130_1-HE.noGEN.end	GA130_1-HE.noGEN.end.gen	percent
uq reads:	2186896	986622	45.1152%
   reads: 	2478728	1106615	44.6445%
----------------
match_TE:2:
  reads:	GA130_1-HE.noGEN.end	GA130_1-HE.noGEN.end.TE	percent
uq reads:	2186896	120295	5.5007%
   reads: 	2478728	137454	5.5453%
----------------
Candidate insertion sites in file: GA130_1-HE_insert.txt
  reads:	26905
  uqreads:	23059
  Number of Candidate sites:	23059

Level 1 collapse of insertion sites in file: GA130_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	674

Level 1 annotation file: GA130_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
GA130_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	GA130_1-HE.noGEN.front	GA130_1-HE.noGEN.front.gendel	percent
uq reads:	2186896	1075790	49.1926%
   reads: 	2478728	1185361	47.8213%
----------------
match_dm6_mask_gen_del:1:
  reads:	GA130_1-HE.noGEN.end	GA130_1-HE.noGEN.end.gendel	percent
uq reads:	2186896	986622	45.1152%
   reads: 	2478728	1106615	44.6445%
----------------
Candidate breakpoint sites in file: GA130_1-HE_depletion.xls
  reads:	63339
  uqreads:	54571
  Number of reads supporting candidate sites:	54571

Level 1 collapse of depletion sites in file: GA130_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	2893