Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-399.fastq.uq.polyn	RAL-399.filter	percent
uq reads:	13784852	1983523	14.3891%
   reads: 	14419578	2105815	14.6039%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-399.filter	RAL-399.nostrna	percent
uq reads:	1983523	1964659	99.0490%
   reads: 	2105815	2079654	98.7577%
----------------
TE_filter:
  reads:	RAL-399.nostrna	RAL-399.noTE	percent
uq reads:	1964659	1961403	99.8343%
   reads: 	2079654	2076221	99.8349%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-399.noGEN.front	RAL-399.noGEN.front.gen	percent
uq reads:	1961403	504884	25.7410%
   reads: 	2076221	566796	27.2994%
----------------
match_TE:2:
  reads:	RAL-399.noGEN.front	RAL-399.noGEN.front.TE	percent
uq reads:	1961403	68662	3.5007%
   reads: 	2076221	70155	3.3790%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-399.noGEN.end	RAL-399.noGEN.end.gen	percent
uq reads:	1961403	181790	9.2684%
   reads: 	2076221	232899	11.2174%
----------------
match_TE:2:
  reads:	RAL-399.noGEN.end	RAL-399.noGEN.end.TE	percent
uq reads:	1961403	37852	1.9298%
   reads: 	2076221	39853	1.9195%
----------------
Candidate insertion sites in file: RAL-399_insert.txt
  reads:	3105
  uqreads:	3084
  Number of Candidate sites:	3084

Level 1 collapse of insertion sites in file: RAL-399_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	217

Level 1 annotation file: RAL-399_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-399_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-399.noGEN.front	RAL-399.noGEN.front.gendel	percent
uq reads:	1961403	504884	25.7410%
   reads: 	2076221	566796	27.2994%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-399.noGEN.end	RAL-399.noGEN.end.gendel	percent
uq reads:	1961403	181790	9.2684%
   reads: 	2076221	232899	11.2174%
----------------
Candidate breakpoint sites in file: RAL-399_depletion.xls
  reads:	6812
  uqreads:	6583
  Number of reads supporting candidate sites:	6583

Level 1 collapse of depletion sites in file: RAL-399_depletion_level1.xls
  Number of Level 1 collapsed sites:	447