Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-239.fastq.uq.polyn	RAL-239.filter	percent
uq reads:	32275844	1926777	5.9697%
   reads: 	34239826	2248384	6.5666%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-239.filter	RAL-239.nostrna	percent
uq reads:	1926777	1820648	94.4919%
   reads: 	2248384	2135584	94.9831%
----------------
TE_filter:
  reads:	RAL-239.nostrna	RAL-239.noTE	percent
uq reads:	1820648	1804641	99.1208%
   reads: 	2135584	2116060	99.0858%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-239.noGEN.front	RAL-239.noGEN.front.gen	percent
uq reads:	1804641	425942	23.6026%
   reads: 	2116060	591800	27.9671%
----------------
match_TE:2:
  reads:	RAL-239.noGEN.front	RAL-239.noGEN.front.TE	percent
uq reads:	1804641	71372	3.9549%
   reads: 	2116060	74428	3.5173%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-239.noGEN.end	RAL-239.noGEN.end.gen	percent
uq reads:	1804641	366559	20.3120%
   reads: 	2116060	530599	25.0749%
----------------
match_TE:2:
  reads:	RAL-239.noGEN.end	RAL-239.noGEN.end.TE	percent
uq reads:	1804641	65661	3.6385%
   reads: 	2116060	68748	3.2489%
----------------
Candidate insertion sites in file: RAL-239_insert.txt
  reads:	5759
  uqreads:	5660
  Number of Candidate sites:	5660

Level 1 collapse of insertion sites in file: RAL-239_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	445

Level 1 annotation file: RAL-239_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-239_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-239.noGEN.front	RAL-239.noGEN.front.gendel	percent
uq reads:	1804641	432803	23.9828%
   reads: 	2116060	608135	28.7390%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-239.noGEN.end	RAL-239.noGEN.end.gendel	percent
uq reads:	1804641	374840	20.7709%
   reads: 	2116060	549157	25.9519%
----------------
Candidate breakpoint sites in file: RAL-239_depletion.xls
  reads:	14107
  uqreads:	13754
  Number of reads supporting candidate sites:	13754

Level 1 collapse of depletion sites in file: RAL-239_depletion_level1.xls
  Number of Level 1 collapsed sites:	1353