Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-223.fastq.uq.polyn	RAL-223.filter	percent
uq reads:	61357684	10128423	16.5072%
   reads: 	70239578	13704085	19.5105%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-223.filter	RAL-223.nostrna	percent
uq reads:	10128423	6178460	61.0012%
   reads: 	13704085	6847358	49.9658%
----------------
TE_filter:
  reads:	RAL-223.nostrna	RAL-223.noTE	percent
uq reads:	6178460	6159572	99.6943%
   reads: 	6847358	6810226	99.4577%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-223.noGEN.front	RAL-223.noGEN.front.gen	percent
uq reads:	6159572	1565901	25.4222%
   reads: 	6810226	1731808	25.4295%
----------------
match_TE:2:
  reads:	RAL-223.noGEN.front	RAL-223.noGEN.front.TE	percent
uq reads:	6159572	268660	4.3617%
   reads: 	6810226	283551	4.1636%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-223.noGEN.end	RAL-223.noGEN.end.gen	percent
uq reads:	6159572	1002337	16.2728%
   reads: 	6810226	1165412	17.1127%
----------------
match_TE:2:
  reads:	RAL-223.noGEN.end	RAL-223.noGEN.end.TE	percent
uq reads:	6159572	198576	3.2239%
   reads: 	6810226	213620	3.1368%
----------------
Candidate insertion sites in file: RAL-223_insert.txt
  reads:	46714
  uqreads:	44840
  Number of Candidate sites:	44840

Level 1 collapse of insertion sites in file: RAL-223_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	846

Level 1 annotation file: RAL-223_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-223_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-223.noGEN.front	RAL-223.noGEN.front.gendel	percent
uq reads:	6159572	1565901	25.4222%
   reads: 	6810226	1731808	25.4295%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-223.noGEN.end	RAL-223.noGEN.end.gendel	percent
uq reads:	6159572	1002337	16.2728%
   reads: 	6810226	1165412	17.1127%
----------------
Candidate breakpoint sites in file: RAL-223_depletion.xls
  reads:	98489
  uqreads:	94283
  Number of reads supporting candidate sites:	94283

Level 1 collapse of depletion sites in file: RAL-223_depletion_level1.xls
  Number of Level 1 collapsed sites:	4023