Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-309.fastq.uq.polyn	RAL-309.filter	percent
uq reads:	32538976	1987757	6.1088%
   reads: 	33561107	2167529	6.4585%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-309.filter	RAL-309.nostrna	percent
uq reads:	1987757	1909838	96.0801%
   reads: 	2167529	2085364	96.2093%
----------------
TE_filter:
  reads:	RAL-309.nostrna	RAL-309.noTE	percent
uq reads:	1909838	1894738	99.2094%
   reads: 	2085364	2068973	99.2140%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-309.noGEN.front	RAL-309.noGEN.front.gen	percent
uq reads:	1894738	679836	35.8802%
   reads: 	2068973	789380	38.1532%
----------------
match_TE:2:
  reads:	RAL-309.noGEN.front	RAL-309.noGEN.front.TE	percent
uq reads:	1894738	71891	3.7942%
   reads: 	2068973	73375	3.5464%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-309.noGEN.end	RAL-309.noGEN.end.gen	percent
uq reads:	1894738	600021	31.6678%
   reads: 	2068973	703041	33.9802%
----------------
match_TE:2:
  reads:	RAL-309.noGEN.end	RAL-309.noGEN.end.TE	percent
uq reads:	1894738	70327	3.7117%
   reads: 	2068973	72125	3.4860%
----------------
Candidate insertion sites in file: RAL-309_insert.txt
  reads:	6402
  uqreads:	6343
  Number of Candidate sites:	6343

Level 1 collapse of insertion sites in file: RAL-309_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	451

Level 1 annotation file: RAL-309_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-309_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-309.noGEN.front	RAL-309.noGEN.front.gendel	percent
uq reads:	1894738	679836	35.8802%
   reads: 	2068973	789380	38.1532%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-309.noGEN.end	RAL-309.noGEN.end.gendel	percent
uq reads:	1894738	600021	31.6678%
   reads: 	2068973	703041	33.9802%
----------------
Candidate breakpoint sites in file: RAL-309_depletion.xls
  reads:	14412
  uqreads:	14141
  Number of reads supporting candidate sites:	14141

Level 1 collapse of depletion sites in file: RAL-309_depletion_level1.xls
  Number of Level 1 collapsed sites:	1227