Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-822.fastq.uq.polyn	RAL-822.filter	percent
uq reads:	37266811	6108486	16.3912%
   reads: 	40387286	7484957	18.5330%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-822.filter	RAL-822.nostrna	percent
uq reads:	6108486	3534447	57.8613%
   reads: 	7484957	4611973	61.6166%
----------------
TE_filter:
  reads:	RAL-822.nostrna	RAL-822.noTE	percent
uq reads:	3534447	3521533	99.6346%
   reads: 	4611973	4598569	99.7094%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-822.noGEN.front	RAL-822.noGEN.front.gen	percent
uq reads:	3521533	915421	25.9950%
   reads: 	4598569	1076037	23.3994%
----------------
match_TE:2:
  reads:	RAL-822.noGEN.front	RAL-822.noGEN.front.TE	percent
uq reads:	3521533	129888	3.6884%
   reads: 	4598569	140579	3.0570%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-822.noGEN.end	RAL-822.noGEN.end.gen	percent
uq reads:	3521533	639712	18.1657%
   reads: 	4598569	782115	17.0078%
----------------
match_TE:2:
  reads:	RAL-822.noGEN.end	RAL-822.noGEN.end.TE	percent
uq reads:	3521533	113990	3.2369%
   reads: 	4598569	127043	2.7627%
----------------
Candidate insertion sites in file: RAL-822_insert.txt
  reads:	15058
  uqreads:	14803
  Number of Candidate sites:	14803

Level 1 collapse of insertion sites in file: RAL-822_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	583

Level 1 annotation file: RAL-822_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-822_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-822.noGEN.front	RAL-822.noGEN.front.gendel	percent
uq reads:	3521533	915421	25.9950%
   reads: 	4598569	1076037	23.3994%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-822.noGEN.end	RAL-822.noGEN.end.gendel	percent
uq reads:	3521533	639712	18.1657%
   reads: 	4598569	782115	17.0078%
----------------
Candidate breakpoint sites in file: RAL-822_depletion.xls
  reads:	35082
  uqreads:	34602
  Number of reads supporting candidate sites:	34602

Level 1 collapse of depletion sites in file: RAL-822_depletion_level1.xls
  Number of Level 1 collapsed sites:	2774