Insertion Pipeline
Bowtie2_wholegenome:
  reads:	OreR-BG.fastq.uq.polyn	OreR-BG.filter	percent
uq reads:	32947209	1425343	4.3261%
   reads: 	37435733	1913097	5.1104%
----------------
virus_structural_rna_repbase_filter:
  reads:	OreR-BG.filter	OreR-BG.nostrna	percent
uq reads:	1425343	1377625	96.6522%
   reads: 	1913097	1829703	95.6409%
----------------
TE_filter:
  reads:	OreR-BG.nostrna	OreR-BG.noTE	percent
uq reads:	1377625	1362351	98.8913%
   reads: 	1829703	1790728	97.8699%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-BG.noGEN.front	OreR-BG.noGEN.front.gen	percent
uq reads:	1362351	435263	31.9494%
   reads: 	1790728	657893	36.7389%
----------------
match_TE:2:
  reads:	OreR-BG.noGEN.front	OreR-BG.noGEN.front.TE	percent
uq reads:	1362351	68460	5.0251%
   reads: 	1790728	75240	4.2016%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-BG.noGEN.end	OreR-BG.noGEN.end.gen	percent
uq reads:	1362351	383243	28.1310%
   reads: 	1790728	602487	33.6448%
----------------
match_TE:2:
  reads:	OreR-BG.noGEN.end	OreR-BG.noGEN.end.TE	percent
uq reads:	1362351	63455	4.6578%
   reads: 	1790728	70374	3.9299%
----------------
Candidate insertion sites in file: OreR-BG_insert.txt
  reads:	9869
  uqreads:	9466
  Number of Candidate sites:	9466

Level 1 collapse of insertion sites in file: OreR-BG_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	693

Level 1 annotation file: OreR-BG_level1siteannotation.xls
Insertion sites in fixed bin:
OreR-BG_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	OreR-BG.noGEN.front	OreR-BG.noGEN.front.gendel	percent
uq reads:	1362351	435263	31.9494%
   reads: 	1790728	657893	36.7389%
----------------
match_dm6_mask_gen_del:1:
  reads:	OreR-BG.noGEN.end	OreR-BG.noGEN.end.gendel	percent
uq reads:	1362351	383243	28.1310%
   reads: 	1790728	602487	33.6448%
----------------
Candidate breakpoint sites in file: OreR-BG_depletion.xls
  reads:	17945
  uqreads:	17036
  Number of reads supporting candidate sites:	17036

Level 1 collapse of depletion sites in file: OreR-BG_depletion_level1.xls
  Number of Level 1 collapsed sites:	1766