Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-409_125b.fastq.uq.polyn	RAL-409_125b.filter	percent
uq reads:	40539139	6404768	15.7990%
   reads: 	43457827	7263684	16.7143%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-409_125b.filter	RAL-409_125b.nostrna	percent
uq reads:	6404768	4919394	76.8083%
   reads: 	7263684	5500784	75.7299%
----------------
TE_filter:
  reads:	RAL-409_125b.nostrna	RAL-409_125b.noTE	percent
uq reads:	4919394	4910334	99.8158%
   reads: 	5500784	5490561	99.8142%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-409_125b.noGEN.front	RAL-409_125b.noGEN.front.gen	percent
uq reads:	4910334	1914823	38.9958%
   reads: 	5490561	2124812	38.6994%
----------------
match_TE:2:
  reads:	RAL-409_125b.noGEN.front	RAL-409_125b.noGEN.front.TE	percent
uq reads:	4910334	279215	5.6863%
   reads: 	5490561	285084	5.1923%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-409_125b.noGEN.end	RAL-409_125b.noGEN.end.gen	percent
uq reads:	4910334	456789	9.3026%
   reads: 	5490561	650843	11.8539%
----------------
match_TE:2:
  reads:	RAL-409_125b.noGEN.end	RAL-409_125b.noGEN.end.TE	percent
uq reads:	4910334	88891	1.8103%
   reads: 	5490561	93911	1.7104%
----------------
Candidate insertion sites in file: RAL-409_125b_insert.txt
  reads:	18565
  uqreads:	18307
  Number of Candidate sites:	18307

Level 1 collapse of insertion sites in file: RAL-409_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	660

Level 1 annotation file: RAL-409_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-409_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-409_125b.noGEN.front	RAL-409_125b.noGEN.front.gendel	percent
uq reads:	4910334	1914823	38.9958%
   reads: 	5490561	2124812	38.6994%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-409_125b.noGEN.end	RAL-409_125b.noGEN.end.gendel	percent
uq reads:	4910334	456789	9.3026%
   reads: 	5490561	650843	11.8539%
----------------
Candidate breakpoint sites in file: RAL-409_125b_depletion.xls
  reads:	46351
  uqreads:	45393
  Number of reads supporting candidate sites:	45393

Level 1 collapse of depletion sites in file: RAL-409_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3365