Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-509.fastq.uq.polyn	RAL-509.filter	percent
uq reads:	35646623	2647996	7.4285%
   reads: 	37488677	2826047	7.5384%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-509.filter	RAL-509.nostrna	percent
uq reads:	2647996	2463004	93.0139%
   reads: 	2826047	2615125	92.5365%
----------------
TE_filter:
  reads:	RAL-509.nostrna	RAL-509.noTE	percent
uq reads:	2463004	2447355	99.3646%
   reads: 	2615125	2596924	99.3040%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-509.noGEN.front	RAL-509.noGEN.front.gen	percent
uq reads:	2447355	905677	37.0064%
   reads: 	2596924	978647	37.6849%
----------------
match_TE:2:
  reads:	RAL-509.noGEN.front	RAL-509.noGEN.front.TE	percent
uq reads:	2447355	119497	4.8827%
   reads: 	2596924	121521	4.6794%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-509.noGEN.end	RAL-509.noGEN.end.gen	percent
uq reads:	2447355	745976	30.4809%
   reads: 	2596924	817824	31.4920%
----------------
match_TE:2:
  reads:	RAL-509.noGEN.end	RAL-509.noGEN.end.TE	percent
uq reads:	2447355	126841	5.1828%
   reads: 	2596924	129185	4.9745%
----------------
Candidate insertion sites in file: RAL-509_insert.txt
  reads:	9611
  uqreads:	9460
  Number of Candidate sites:	9460

Level 1 collapse of insertion sites in file: RAL-509_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	481

Level 1 annotation file: RAL-509_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-509_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-509.noGEN.front	RAL-509.noGEN.front.gendel	percent
uq reads:	2447355	905677	37.0064%
   reads: 	2596924	978647	37.6849%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-509.noGEN.end	RAL-509.noGEN.end.gendel	percent
uq reads:	2447355	745976	30.4809%
   reads: 	2596924	817824	31.4920%
----------------
Candidate breakpoint sites in file: RAL-509_depletion.xls
  reads:	20986
  uqreads:	20537
  Number of reads supporting candidate sites:	20537

Level 1 collapse of depletion sites in file: RAL-509_depletion_level1.xls
  Number of Level 1 collapsed sites:	1935