Insertion Pipeline
Bowtie2_wholegenome:
  reads:	OreR-PB2.fastq.uq.polyn	OreR-PB2.filter	percent
uq reads:	18144517	1275842	7.0316%
   reads: 	19507463	1583696	8.1184%
----------------
virus_structural_rna_repbase_filter:
  reads:	OreR-PB2.filter	OreR-PB2.nostrna	percent
uq reads:	1275842	1240836	97.2562%
   reads: 	1583696	1507726	95.2030%
----------------
TE_filter:
  reads:	OreR-PB2.nostrna	OreR-PB2.noTE	percent
uq reads:	1240836	1240659	99.9857%
   reads: 	1507726	1507549	99.9883%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-PB2.noGEN.front	OreR-PB2.noGEN.front.gen	percent
uq reads:	1240659	391174	31.5295%
   reads: 	1507549	454806	30.1686%
----------------
match_TE:2:
  reads:	OreR-PB2.noGEN.front	OreR-PB2.noGEN.front.TE	percent
uq reads:	1240659	59376	4.7858%
   reads: 	1507549	61217	4.0607%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-PB2.noGEN.end	OreR-PB2.noGEN.end.gen	percent
uq reads:	1240659	220098	17.7404%
   reads: 	1507549	273915	18.1696%
----------------
match_TE:2:
  reads:	OreR-PB2.noGEN.end	OreR-PB2.noGEN.end.TE	percent
uq reads:	1240659	46809	3.7729%
   reads: 	1507549	48984	3.2492%
----------------
Candidate insertion sites in file: OreR-PB2_insert.txt
  reads:	11946
  uqreads:	11770
  Number of Candidate sites:	11770

Level 1 collapse of insertion sites in file: OreR-PB2_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	828

Level 1 annotation file: OreR-PB2_level1siteannotation.xls
Insertion sites in fixed bin:
OreR-PB2_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	OreR-PB2.noGEN.front	OreR-PB2.noGEN.front.gendel	percent
uq reads:	1240659	391174	31.5295%
   reads: 	1507549	454806	30.1686%
----------------
match_dm6_mask_gen_del:1:
  reads:	OreR-PB2.noGEN.end	OreR-PB2.noGEN.end.gendel	percent
uq reads:	1240659	220098	17.7404%
   reads: 	1507549	273915	18.1696%
----------------
Candidate breakpoint sites in file: OreR-PB2_depletion.xls
  reads:	25599
  uqreads:	24366
  Number of reads supporting candidate sites:	24366

Level 1 collapse of depletion sites in file: OreR-PB2_depletion_level1.xls
  Number of Level 1 collapsed sites:	2652