Insertion Pipeline
Bowtie2_wholegenome:
  reads:	OreR-TO2.fastq.uq.polyn	OreR-TO2.filter	percent
uq reads:	62235317	3885458	6.2432%
   reads: 	71014054	5267076	7.4169%
----------------
virus_structural_rna_repbase_filter:
  reads:	OreR-TO2.filter	OreR-TO2.nostrna	percent
uq reads:	3885458	3827755	98.5149%
   reads: 	5267076	5008481	95.0903%
----------------
TE_filter:
  reads:	OreR-TO2.nostrna	OreR-TO2.noTE	percent
uq reads:	3827755	3800164	99.2792%
   reads: 	5008481	4922912	98.2915%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-TO2.noGEN.front	OreR-TO2.noGEN.front.gen	percent
uq reads:	3800164	1397259	36.7684%
   reads: 	4922912	1663406	33.7891%
----------------
match_TE:2:
  reads:	OreR-TO2.noGEN.front	OreR-TO2.noGEN.front.TE	percent
uq reads:	3800164	202754	5.3354%
   reads: 	4922912	220838	4.4859%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-TO2.noGEN.end	OreR-TO2.noGEN.end.gen	percent
uq reads:	3800164	614805	16.1784%
   reads: 	4922912	841519	17.0939%
----------------
match_TE:2:
  reads:	OreR-TO2.noGEN.end	OreR-TO2.noGEN.end.TE	percent
uq reads:	3800164	148308	3.9027%
   reads: 	4922912	167498	3.4024%
----------------
Candidate insertion sites in file: OreR-TO2_insert.txt
  reads:	39448
  uqreads:	37690
  Number of Candidate sites:	37690

Level 1 collapse of insertion sites in file: OreR-TO2_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1013

Level 1 annotation file: OreR-TO2_level1siteannotation.xls
Insertion sites in fixed bin:
OreR-TO2_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	OreR-TO2.noGEN.front	OreR-TO2.noGEN.front.gendel	percent
uq reads:	3800164	1397259	36.7684%
   reads: 	4922912	1663406	33.7891%
----------------
match_dm6_mask_gen_del:1:
  reads:	OreR-TO2.noGEN.end	OreR-TO2.noGEN.end.gendel	percent
uq reads:	3800164	614805	16.1784%
   reads: 	4922912	841519	17.0939%
----------------
Candidate breakpoint sites in file: OreR-TO2_depletion.xls
  reads:	70801
  uqreads:	65631
  Number of reads supporting candidate sites:	65631

Level 1 collapse of depletion sites in file: OreR-TO2_depletion_level1.xls
  Number of Level 1 collapsed sites:	4807