Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-783.fastq.uq.polyn	RAL-783.filter	percent
uq reads:	32987423	4020490	12.1879%
   reads: 	36217557	5546275	15.3138%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-783.filter	RAL-783.nostrna	percent
uq reads:	4020490	1446246	35.9719%
   reads: 	5546275	1700764	30.6650%
----------------
TE_filter:
  reads:	RAL-783.nostrna	RAL-783.noTE	percent
uq reads:	1446246	1437014	99.3617%
   reads: 	1700764	1687943	99.2462%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-783.noGEN.front	RAL-783.noGEN.front.gen	percent
uq reads:	1437014	514721	35.8188%
   reads: 	1687943	653094	38.6917%
----------------
match_TE:2:
  reads:	RAL-783.noGEN.front	RAL-783.noGEN.front.TE	percent
uq reads:	1437014	71653	4.9862%
   reads: 	1687943	74268	4.3999%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-783.noGEN.end	RAL-783.noGEN.end.gen	percent
uq reads:	1437014	437182	30.4229%
   reads: 	1687943	567976	33.6490%
----------------
match_TE:2:
  reads:	RAL-783.noGEN.end	RAL-783.noGEN.end.TE	percent
uq reads:	1437014	70202	4.8853%
   reads: 	1687943	73074	4.3292%
----------------
Candidate insertion sites in file: RAL-783_insert.txt
  reads:	7690
  uqreads:	7521
  Number of Candidate sites:	7521

Level 1 collapse of insertion sites in file: RAL-783_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	459

Level 1 annotation file: RAL-783_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-783_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-783.noGEN.front	RAL-783.noGEN.front.gendel	percent
uq reads:	1437014	514721	35.8188%
   reads: 	1687943	653094	38.6917%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-783.noGEN.end	RAL-783.noGEN.end.gendel	percent
uq reads:	1437014	437182	30.4229%
   reads: 	1687943	567976	33.6490%
----------------
Candidate breakpoint sites in file: RAL-783_depletion.xls
  reads:	17780
  uqreads:	17263
  Number of reads supporting candidate sites:	17263

Level 1 collapse of depletion sites in file: RAL-783_depletion_level1.xls
  Number of Level 1 collapsed sites:	1639