Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-21.fastq.uq.polyn	RAL-21.filter	percent
uq reads:	32599357	5867410	17.9985%
   reads: 	36113305	7750211	21.4608%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-21.filter	RAL-21.nostrna	percent
uq reads:	5867410	1853763	31.5942%
   reads: 	7750211	2136340	27.5649%
----------------
TE_filter:
  reads:	RAL-21.nostrna	RAL-21.noTE	percent
uq reads:	1853763	1842928	99.4155%
   reads: 	2136340	2123137	99.3820%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-21.noGEN.front	RAL-21.noGEN.front.gen	percent
uq reads:	1842928	545544	29.6020%
   reads: 	2123137	604608	28.4771%
----------------
match_TE:2:
  reads:	RAL-21.noGEN.front	RAL-21.noGEN.front.TE	percent
uq reads:	1842928	80075	4.3450%
   reads: 	2123137	86121	4.0563%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-21.noGEN.end	RAL-21.noGEN.end.gen	percent
uq reads:	1842928	436514	23.6859%
   reads: 	2123137	494524	23.2921%
----------------
match_TE:2:
  reads:	RAL-21.noGEN.end	RAL-21.noGEN.end.TE	percent
uq reads:	1842928	69741	3.7842%
   reads: 	2123137	75899	3.5749%
----------------
Candidate insertion sites in file: RAL-21_insert.txt
  reads:	12877
  uqreads:	12615
  Number of Candidate sites:	12615

Level 1 collapse of insertion sites in file: RAL-21_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	690

Level 1 annotation file: RAL-21_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-21_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-21.noGEN.front	RAL-21.noGEN.front.gendel	percent
uq reads:	1842928	555370	30.1352%
   reads: 	2123137	617429	29.0810%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-21.noGEN.end	RAL-21.noGEN.end.gendel	percent
uq reads:	1842928	443562	24.0683%
   reads: 	2123137	504237	23.7496%
----------------
Candidate breakpoint sites in file: RAL-21_depletion.xls
  reads:	28657
  uqreads:	27887
  Number of reads supporting candidate sites:	27887

Level 1 collapse of depletion sites in file: RAL-21_depletion_level1.xls
  Number of Level 1 collapsed sites:	2591