Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-381.fastq.uq.polyn	RAL-381.filter	percent
uq reads:	49903787	4410963	8.8389%
   reads: 	53531083	4974790	9.2933%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-381.filter	RAL-381.nostrna	percent
uq reads:	4410963	4289404	97.2442%
   reads: 	4974790	4832978	97.1494%
----------------
TE_filter:
  reads:	RAL-381.nostrna	RAL-381.noTE	percent
uq reads:	4289404	4268504	99.5128%
   reads: 	4832978	4805876	99.4392%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-381.noGEN.front	RAL-381.noGEN.front.gen	percent
uq reads:	4268504	1271154	29.7798%
   reads: 	4805876	1596452	33.2188%
----------------
match_TE:2:
  reads:	RAL-381.noGEN.front	RAL-381.noGEN.front.TE	percent
uq reads:	4268504	167843	3.9321%
   reads: 	4805876	175209	3.6457%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-381.noGEN.end	RAL-381.noGEN.end.gen	percent
uq reads:	4268504	948769	22.2272%
   reads: 	4805876	1253910	26.0912%
----------------
match_TE:2:
  reads:	RAL-381.noGEN.end	RAL-381.noGEN.end.TE	percent
uq reads:	4268504	141061	3.3047%
   reads: 	4805876	149420	3.1091%
----------------
Candidate insertion sites in file: RAL-381_insert.txt
  reads:	14462
  uqreads:	14114
  Number of Candidate sites:	14114

Level 1 collapse of insertion sites in file: RAL-381_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	613

Level 1 annotation file: RAL-381_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-381_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-381.noGEN.front	RAL-381.noGEN.front.gendel	percent
uq reads:	4268504	1271154	29.7798%
   reads: 	4805876	1596452	33.2188%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-381.noGEN.end	RAL-381.noGEN.end.gendel	percent
uq reads:	4268504	948769	22.2272%
   reads: 	4805876	1253910	26.0912%
----------------
Candidate breakpoint sites in file: RAL-381_depletion.xls
  reads:	31652
  uqreads:	30427
  Number of reads supporting candidate sites:	30427

Level 1 collapse of depletion sites in file: RAL-381_depletion_level1.xls
  Number of Level 1 collapsed sites:	2311