Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-365.fastq.uq.polyn	RAL-365.filter	percent
uq reads:	30370321	5961393	19.6290%
   reads: 	32138087	6335504	19.7134%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-365.filter	RAL-365.nostrna	percent
uq reads:	5961393	5267553	88.3611%
   reads: 	6335504	5573967	87.9799%
----------------
TE_filter:
  reads:	RAL-365.nostrna	RAL-365.noTE	percent
uq reads:	5267553	5260958	99.8748%
   reads: 	5573967	5566524	99.8665%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-365.noGEN.front	RAL-365.noGEN.front.gen	percent
uq reads:	5260958	1374467	26.1258%
   reads: 	5566524	1524945	27.3949%
----------------
match_TE:2:
  reads:	RAL-365.noGEN.front	RAL-365.noGEN.front.TE	percent
uq reads:	5260958	191884	3.6473%
   reads: 	5566524	195708	3.5158%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-365.noGEN.end	RAL-365.noGEN.end.gen	percent
uq reads:	5260958	363930	6.9176%
   reads: 	5566524	501505	9.0093%
----------------
match_TE:2:
  reads:	RAL-365.noGEN.end	RAL-365.noGEN.end.TE	percent
uq reads:	5260958	78102	1.4846%
   reads: 	5566524	82367	1.4797%
----------------
Candidate insertion sites in file: RAL-365_insert.txt
  reads:	6678
  uqreads:	6569
  Number of Candidate sites:	6569

Level 1 collapse of insertion sites in file: RAL-365_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	389

Level 1 annotation file: RAL-365_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-365_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-365.noGEN.front	RAL-365.noGEN.front.gendel	percent
uq reads:	5260958	1374467	26.1258%
   reads: 	5566524	1524945	27.3949%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-365.noGEN.end	RAL-365.noGEN.end.gendel	percent
uq reads:	5260958	363930	6.9176%
   reads: 	5566524	501505	9.0093%
----------------
Candidate breakpoint sites in file: RAL-365_depletion.xls
  reads:	15771
  uqreads:	15004
  Number of reads supporting candidate sites:	15004

Level 1 collapse of depletion sites in file: RAL-365_depletion_level1.xls
  Number of Level 1 collapsed sites:	1591