Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-897.fastq.uq.polyn	RAL-897.filter	percent
uq reads:	64850732	7151794	11.0281%
   reads: 	70019220	8108179	11.5799%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-897.filter	RAL-897.nostrna	percent
uq reads:	7151794	4455430	62.2981%
   reads: 	8108179	4856115	59.8916%
----------------
TE_filter:
  reads:	RAL-897.nostrna	RAL-897.noTE	percent
uq reads:	4455430	4432775	99.4915%
   reads: 	4856115	4829636	99.4547%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-897.noGEN.front	RAL-897.noGEN.front.gen	percent
uq reads:	4432775	1094069	24.6814%
   reads: 	4829636	1282647	26.5578%
----------------
match_TE:2:
  reads:	RAL-897.noGEN.front	RAL-897.noGEN.front.TE	percent
uq reads:	4432775	141264	3.1868%
   reads: 	4829636	149023	3.0856%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-897.noGEN.end	RAL-897.noGEN.end.gen	percent
uq reads:	4432775	1070208	24.1431%
   reads: 	4829636	1254742	25.9801%
----------------
match_TE:2:
  reads:	RAL-897.noGEN.end	RAL-897.noGEN.end.TE	percent
uq reads:	4432775	162340	3.6623%
   reads: 	4829636	170956	3.5397%
----------------
Candidate insertion sites in file: RAL-897_insert.txt
  reads:	12414
  uqreads:	12053
  Number of Candidate sites:	12053

Level 1 collapse of insertion sites in file: RAL-897_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	572

Level 1 annotation file: RAL-897_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-897_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-897.noGEN.front	RAL-897.noGEN.front.gendel	percent
uq reads:	4432775	1094069	24.6814%
   reads: 	4829636	1282647	26.5578%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-897.noGEN.end	RAL-897.noGEN.end.gendel	percent
uq reads:	4432775	1070208	24.1431%
   reads: 	4829636	1254742	25.9801%
----------------
Candidate breakpoint sites in file: RAL-897_depletion.xls
  reads:	28278
  uqreads:	27229
  Number of reads supporting candidate sites:	27229

Level 1 collapse of depletion sites in file: RAL-897_depletion_level1.xls
  Number of Level 1 collapsed sites:	2353