Insertion Pipeline
Bowtie2_wholegenome:
  reads:	OreR-PB1.fastq.uq.polyn	OreR-PB1.filter	percent
uq reads:	65253573	4154474	6.3667%
   reads: 	75049391	6006706	8.0037%
----------------
virus_structural_rna_repbase_filter:
  reads:	OreR-PB1.filter	OreR-PB1.nostrna	percent
uq reads:	4154474	4073225	98.0443%
   reads: 	6006706	5636136	93.8307%
----------------
TE_filter:
  reads:	OreR-PB1.nostrna	OreR-PB1.noTE	percent
uq reads:	4073225	4072491	99.9820%
   reads: 	5636136	5635395	99.9869%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-PB1.noGEN.front	OreR-PB1.noGEN.front.gen	percent
uq reads:	4072491	1550774	38.0792%
   reads: 	5635395	1835583	32.5724%
----------------
match_TE:2:
  reads:	OreR-PB1.noGEN.front	OreR-PB1.noGEN.front.TE	percent
uq reads:	4072491	207610	5.0979%
   reads: 	5635395	220781	3.9178%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-PB1.noGEN.end	OreR-PB1.noGEN.end.gen	percent
uq reads:	4072491	685125	16.8232%
   reads: 	5635395	933538	16.5656%
----------------
match_TE:2:
  reads:	OreR-PB1.noGEN.end	OreR-PB1.noGEN.end.TE	percent
uq reads:	4072491	134722	3.3081%
   reads: 	5635395	148365	2.6327%
----------------
Candidate insertion sites in file: OreR-PB1_insert.txt
  reads:	37767
  uqreads:	36356
  Number of Candidate sites:	36356

Level 1 collapse of insertion sites in file: OreR-PB1_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1399

Level 1 annotation file: OreR-PB1_level1siteannotation.xls
Insertion sites in fixed bin:
OreR-PB1_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	OreR-PB1.noGEN.front	OreR-PB1.noGEN.front.gendel	percent
uq reads:	4072491	1550774	38.0792%
   reads: 	5635395	1835583	32.5724%
----------------
match_dm6_mask_gen_del:1:
  reads:	OreR-PB1.noGEN.end	OreR-PB1.noGEN.end.gendel	percent
uq reads:	4072491	685125	16.8232%
   reads: 	5635395	933538	16.5656%
----------------
Candidate breakpoint sites in file: OreR-PB1_depletion.xls
  reads:	79602
  uqreads:	74659
  Number of reads supporting candidate sites:	74659

Level 1 collapse of depletion sites in file: OreR-PB1_depletion_level1.xls
  Number of Level 1 collapsed sites:	5816