Insertion Pipeline
Bowtie2_wholegenome:
  reads:	OreR-Dw1.fastq.uq.polyn	OreR-Dw1.filter	percent
uq reads:	48421144	1643980	3.3952%
   reads: 	68796798	4600311	6.6868%
----------------
virus_structural_rna_repbase_filter:
  reads:	OreR-Dw1.filter	OreR-Dw1.nostrna	percent
uq reads:	1643980	1624805	98.8336%
   reads: 	4600311	4572952	99.4053%
----------------
TE_filter:
  reads:	OreR-Dw1.nostrna	OreR-Dw1.noTE	percent
uq reads:	1624805	1622363	99.8497%
   reads: 	4572952	4570051	99.9366%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-Dw1.noGEN.front	OreR-Dw1.noGEN.front.gen	percent
uq reads:	1622363	560564	34.5523%
   reads: 	4570051	1835037	40.1535%
----------------
match_TE:2:
  reads:	OreR-Dw1.noGEN.front	OreR-Dw1.noGEN.front.TE	percent
uq reads:	1622363	120757	7.4433%
   reads: 	4570051	159759	3.4958%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-Dw1.noGEN.end	OreR-Dw1.noGEN.end.gen	percent
uq reads:	1622363	448810	27.6640%
   reads: 	4570051	1697963	37.1541%
----------------
match_TE:2:
  reads:	OreR-Dw1.noGEN.end	OreR-Dw1.noGEN.end.TE	percent
uq reads:	1622363	106738	6.5792%
   reads: 	4570051	143830	3.1472%
----------------
Candidate insertion sites in file: OreR-Dw1_insert.txt
  reads:	12189
  uqreads:	9775
  Number of Candidate sites:	9775

Level 1 collapse of insertion sites in file: OreR-Dw1_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	503

Level 1 annotation file: OreR-Dw1_level1siteannotation.xls
Insertion sites in fixed bin:
OreR-Dw1_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	OreR-Dw1.noGEN.front	OreR-Dw1.noGEN.front.gendel	percent
uq reads:	1622363	560564	34.5523%
   reads: 	4570051	1835037	40.1535%
----------------
match_dm6_mask_gen_del:1:
  reads:	OreR-Dw1.noGEN.end	OreR-Dw1.noGEN.end.gendel	percent
uq reads:	1622363	448810	27.6640%
   reads: 	4570051	1697963	37.1541%
----------------
Candidate breakpoint sites in file: OreR-Dw1_depletion.xls
  reads:	29376
  uqreads:	24091
  Number of reads supporting candidate sites:	24091

Level 1 collapse of depletion sites in file: OreR-Dw1_depletion_level1.xls
  Number of Level 1 collapsed sites:	2074