Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-802_95b.fastq.uq.polyn	RAL-802_95b.filter	percent
uq reads:	22117061	4034625	18.2421%
   reads: 	23779634	4703419	19.7792%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-802_95b.filter	RAL-802_95b.nostrna	percent
uq reads:	4034625	1573220	38.9930%
   reads: 	4703419	1838845	39.0959%
----------------
TE_filter:
  reads:	RAL-802_95b.nostrna	RAL-802_95b.noTE	percent
uq reads:	1573220	1562901	99.3441%
   reads: 	1838845	1827641	99.3907%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-802_95b.noGEN.front	RAL-802_95b.noGEN.front.gen	percent
uq reads:	1562901	383845	24.5598%
   reads: 	1827641	427392	23.3849%
----------------
match_TE:2:
  reads:	RAL-802_95b.noGEN.front	RAL-802_95b.noGEN.front.TE	percent
uq reads:	1562901	45268	2.8964%
   reads: 	1827641	51440	2.8146%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-802_95b.noGEN.end	RAL-802_95b.noGEN.end.gen	percent
uq reads:	1562901	404952	25.9103%
   reads: 	1827641	449648	24.6026%
----------------
match_TE:2:
  reads:	RAL-802_95b.noGEN.end	RAL-802_95b.noGEN.end.TE	percent
uq reads:	1562901	49984	3.1982%
   reads: 	1827641	56366	3.0841%
----------------
Candidate insertion sites in file: RAL-802_95b_insert.txt
  reads:	6893
  uqreads:	6825
  Number of Candidate sites:	6825

Level 1 collapse of insertion sites in file: RAL-802_95b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	465

Level 1 annotation file: RAL-802_95b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-802_95b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-802_95b.noGEN.front	RAL-802_95b.noGEN.front.gendel	percent
uq reads:	1562901	383845	24.5598%
   reads: 	1827641	427392	23.3849%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-802_95b.noGEN.end	RAL-802_95b.noGEN.end.gendel	percent
uq reads:	1562901	404952	25.9103%
   reads: 	1827641	449648	24.6026%
----------------
Candidate breakpoint sites in file: RAL-802_95b_depletion.xls
  reads:	18326
  uqreads:	18163
  Number of reads supporting candidate sites:	18163

Level 1 collapse of depletion sites in file: RAL-802_95b_depletion_level1.xls
  Number of Level 1 collapsed sites:	1664