Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-208.fastq.uq.polyn	RAL-208.filter	percent
uq reads:	44138016	4386451	9.9380%
   reads: 	51968173	4977426	9.5778%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-208.filter	RAL-208.nostrna	percent
uq reads:	4386451	4305966	98.1651%
   reads: 	4977426	4821091	96.8591%
----------------
TE_filter:
  reads:	RAL-208.nostrna	RAL-208.noTE	percent
uq reads:	4305966	4291259	99.6585%
   reads: 	4821091	4802051	99.6051%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-208.noGEN.front	RAL-208.noGEN.front.gen	percent
uq reads:	4291259	2037696	47.4848%
   reads: 	4802051	2203790	45.8927%
----------------
match_TE:2:
  reads:	RAL-208.noGEN.front	RAL-208.noGEN.front.TE	percent
uq reads:	4291259	269482	6.2798%
   reads: 	4802051	286704	5.9704%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-208.noGEN.end	RAL-208.noGEN.end.gen	percent
uq reads:	4291259	755105	17.5964%
   reads: 	4802051	917278	19.1018%
----------------
match_TE:2:
  reads:	RAL-208.noGEN.end	RAL-208.noGEN.end.TE	percent
uq reads:	4291259	142050	3.3102%
   reads: 	4802051	158914	3.3093%
----------------
Candidate insertion sites in file: RAL-208_insert.txt
  reads:	13982
  uqreads:	12476
  Number of Candidate sites:	12476

Level 1 collapse of insertion sites in file: RAL-208_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	518

Level 1 annotation file: RAL-208_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-208_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-208.noGEN.front	RAL-208.noGEN.front.gendel	percent
uq reads:	4291259	2037696	47.4848%
   reads: 	4802051	2203790	45.8927%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-208.noGEN.end	RAL-208.noGEN.end.gendel	percent
uq reads:	4291259	755105	17.5964%
   reads: 	4802051	917278	19.1018%
----------------
Candidate breakpoint sites in file: RAL-208_depletion.xls
  reads:	32224
  uqreads:	27084
  Number of reads supporting candidate sites:	27084

Level 1 collapse of depletion sites in file: RAL-208_depletion_level1.xls
  Number of Level 1 collapsed sites:	2503