Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-317.fastq.uq.polyn	RAL-317.filter	percent
uq reads:	25504022	3199058	12.5433%
   reads: 	26694988	3428082	12.8417%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-317.filter	RAL-317.nostrna	percent
uq reads:	3199058	2460811	76.9230%
   reads: 	3428082	2646539	77.2017%
----------------
TE_filter:
  reads:	RAL-317.nostrna	RAL-317.noTE	percent
uq reads:	2460811	2449090	99.5237%
   reads: 	2646539	2633941	99.5240%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-317.noGEN.front	RAL-317.noGEN.front.gen	percent
uq reads:	2449090	378654	15.4610%
   reads: 	2633941	501675	19.0466%
----------------
match_TE:2:
  reads:	RAL-317.noGEN.front	RAL-317.noGEN.front.TE	percent
uq reads:	2449090	53762	2.1952%
   reads: 	2633941	54953	2.0863%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-317.noGEN.end	RAL-317.noGEN.end.gen	percent
uq reads:	2449090	424980	17.3526%
   reads: 	2633941	544334	20.6661%
----------------
match_TE:2:
  reads:	RAL-317.noGEN.end	RAL-317.noGEN.end.TE	percent
uq reads:	2449090	76617	3.1284%
   reads: 	2633941	78159	2.9674%
----------------
Candidate insertion sites in file: RAL-317_insert.txt
  reads:	4193
  uqreads:	4135
  Number of Candidate sites:	4135

Level 1 collapse of insertion sites in file: RAL-317_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	321

Level 1 annotation file: RAL-317_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-317_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-317.noGEN.front	RAL-317.noGEN.front.gendel	percent
uq reads:	2449090	378654	15.4610%
   reads: 	2633941	501675	19.0466%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-317.noGEN.end	RAL-317.noGEN.end.gendel	percent
uq reads:	2449090	424980	17.3526%
   reads: 	2633941	544334	20.6661%
----------------
Candidate breakpoint sites in file: RAL-317_depletion.xls
  reads:	9802
  uqreads:	9577
  Number of reads supporting candidate sites:	9577

Level 1 collapse of depletion sites in file: RAL-317_depletion_level1.xls
  Number of Level 1 collapsed sites:	743