Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-301_75b.fastq.uq.polyn	RAL-301_75b.filter	percent
uq reads:	43941822	5484461	12.4812%
   reads: 	52250542	6262738	11.9860%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-301_75b.filter	RAL-301_75b.nostrna	percent
uq reads:	5484461	5395707	98.3817%
   reads: 	6262738	6078555	97.0591%
----------------
TE_filter:
  reads:	RAL-301_75b.nostrna	RAL-301_75b.noTE	percent
uq reads:	5395707	5382687	99.7587%
   reads: 	6078555	6061127	99.7133%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-301_75b.noGEN.front	RAL-301_75b.noGEN.front.gen	percent
uq reads:	5382687	2462874	45.7555%
   reads: 	6061127	2663749	43.9481%
----------------
match_TE:2:
  reads:	RAL-301_75b.noGEN.front	RAL-301_75b.noGEN.front.TE	percent
uq reads:	5382687	299604	5.5661%
   reads: 	6061127	316950	5.2292%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-301_75b.noGEN.end	RAL-301_75b.noGEN.end.gen	percent
uq reads:	5382687	762806	14.1715%
   reads: 	6061127	955015	15.7564%
----------------
match_TE:2:
  reads:	RAL-301_75b.noGEN.end	RAL-301_75b.noGEN.end.TE	percent
uq reads:	5382687	130445	2.4234%
   reads: 	6061127	147505	2.4336%
----------------
Candidate insertion sites in file: RAL-301_75b_insert.txt
  reads:	13970
  uqreads:	12072
  Number of Candidate sites:	12072

Level 1 collapse of insertion sites in file: RAL-301_75b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	541

Level 1 annotation file: RAL-301_75b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-301_75b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-301_75b.noGEN.front	RAL-301_75b.noGEN.front.gendel	percent
uq reads:	5382687	2462874	45.7555%
   reads: 	6061127	2663749	43.9481%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-301_75b.noGEN.end	RAL-301_75b.noGEN.end.gendel	percent
uq reads:	5382687	762806	14.1715%
   reads: 	6061127	955015	15.7564%
----------------
Candidate breakpoint sites in file: RAL-301_75b_depletion.xls
  reads:	31013
  uqreads:	25194
  Number of reads supporting candidate sites:	25194

Level 1 collapse of depletion sites in file: RAL-301_75b_depletion_level1.xls
  Number of Level 1 collapsed sites:	2348