Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-513.fastq.uq.polyn	RAL-513.filter	percent
uq reads:	39775977	4164033	10.4687%
   reads: 	41703471	4535022	10.8744%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-513.filter	RAL-513.nostrna	percent
uq reads:	4164033	3156383	75.8011%
   reads: 	4535022	3484263	76.8301%
----------------
TE_filter:
  reads:	RAL-513.nostrna	RAL-513.noTE	percent
uq reads:	3156383	3127552	99.0866%
   reads: 	3484263	3452741	99.0953%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-513.noGEN.front	RAL-513.noGEN.front.gen	percent
uq reads:	3127552	720054	23.0229%
   reads: 	3452741	862666	24.9850%
----------------
match_TE:2:
  reads:	RAL-513.noGEN.front	RAL-513.noGEN.front.TE	percent
uq reads:	3127552	120907	3.8659%
   reads: 	3452741	124063	3.5932%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-513.noGEN.end	RAL-513.noGEN.end.gen	percent
uq reads:	3127552	618575	19.7782%
   reads: 	3452741	752329	21.7893%
----------------
match_TE:2:
  reads:	RAL-513.noGEN.end	RAL-513.noGEN.end.TE	percent
uq reads:	3127552	111886	3.5774%
   reads: 	3452741	115290	3.3391%
----------------
Candidate insertion sites in file: RAL-513_insert.txt
  reads:	13674
  uqreads:	13558
  Number of Candidate sites:	13558

Level 1 collapse of insertion sites in file: RAL-513_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	630

Level 1 annotation file: RAL-513_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-513_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-513.noGEN.front	RAL-513.noGEN.front.gendel	percent
uq reads:	3127552	732290	23.4142%
   reads: 	3452741	879618	25.4759%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-513.noGEN.end	RAL-513.noGEN.end.gendel	percent
uq reads:	3127552	629687	20.1335%
   reads: 	3452741	768452	22.2563%
----------------
Candidate breakpoint sites in file: RAL-513_depletion.xls
  reads:	30107
  uqreads:	29716
  Number of reads supporting candidate sites:	29716

Level 1 collapse of depletion sites in file: RAL-513_depletion_level1.xls
  Number of Level 1 collapsed sites:	2768