Insertion Pipeline
Bowtie2_wholegenome:
  reads:	OreR-TO1.fastq.uq.polyn	OreR-TO1.filter	percent
uq reads:	15504816	991786	6.3966%
   reads: 	16803975	1211561	7.2100%
----------------
virus_structural_rna_repbase_filter:
  reads:	OreR-TO1.filter	OreR-TO1.nostrna	percent
uq reads:	991786	972949	98.1007%
   reads: 	1211561	1162013	95.9104%
----------------
TE_filter:
  reads:	OreR-TO1.nostrna	OreR-TO1.noTE	percent
uq reads:	972949	965077	99.1909%
   reads: 	1162013	1142985	98.3625%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-TO1.noGEN.front	OreR-TO1.noGEN.front.gen	percent
uq reads:	965077	332390	34.4418%
   reads: 	1142985	380495	33.2896%
----------------
match_TE:2:
  reads:	OreR-TO1.noGEN.front	OreR-TO1.noGEN.front.TE	percent
uq reads:	965077	54325	5.6291%
   reads: 	1142985	57179	5.0026%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-TO1.noGEN.end	OreR-TO1.noGEN.end.gen	percent
uq reads:	965077	132795	13.7600%
   reads: 	1142985	170788	14.9423%
----------------
match_TE:2:
  reads:	OreR-TO1.noGEN.end	OreR-TO1.noGEN.end.TE	percent
uq reads:	965077	40496	4.1961%
   reads: 	1142985	44784	3.9182%
----------------
Candidate insertion sites in file: OreR-TO1_insert.txt
  reads:	11406
  uqreads:	11100
  Number of Candidate sites:	11100

Level 1 collapse of insertion sites in file: OreR-TO1_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	761

Level 1 annotation file: OreR-TO1_level1siteannotation.xls
Insertion sites in fixed bin:
OreR-TO1_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	OreR-TO1.noGEN.front	OreR-TO1.noGEN.front.gendel	percent
uq reads:	965077	332390	34.4418%
   reads: 	1142985	380495	33.2896%
----------------
match_dm6_mask_gen_del:1:
  reads:	OreR-TO1.noGEN.end	OreR-TO1.noGEN.end.gendel	percent
uq reads:	965077	132795	13.7600%
   reads: 	1142985	170788	14.9423%
----------------
Candidate breakpoint sites in file: OreR-TO1_depletion.xls
  reads:	20537
  uqreads:	19384
  Number of reads supporting candidate sites:	19384

Level 1 collapse of depletion sites in file: OreR-TO1_depletion_level1.xls
  Number of Level 1 collapsed sites:	2254