Insertion Pipeline
Bowtie2_wholegenome:
  reads:	EG73N.fastq.uq.polyn	EG73N.filter	percent
uq reads:	19292736	1053112	5.4586%
   reads: 	20248918	1146228	5.6607%
----------------
virus_structural_rna_repbase_filter:
  reads:	EG73N.filter	EG73N.nostrna	percent
uq reads:	1053112	829005	78.7195%
   reads: 	1146228	897749	78.3220%
----------------
TE_filter:
  reads:	EG73N.nostrna	EG73N.noTE	percent
uq reads:	829005	825457	99.5720%
   reads: 	897749	893620	99.5401%
----------------
match_dm6_mask_gen:1:
  reads:	EG73N.noGEN.front	EG73N.noGEN.front.gen	percent
uq reads:	825457	315510	38.2225%
   reads: 	893620	326353	36.5203%
----------------
match_TE:2:
  reads:	EG73N.noGEN.front	EG73N.noGEN.front.TE	percent
uq reads:	825457	44064	5.3381%
   reads: 	893620	45100	5.0469%
----------------
match_dm6_mask_gen:1:
  reads:	EG73N.noGEN.end	EG73N.noGEN.end.gen	percent
uq reads:	825457	328636	39.8126%
   reads: 	893620	339643	38.0075%
----------------
match_TE:2:
  reads:	EG73N.noGEN.end	EG73N.noGEN.end.TE	percent
uq reads:	825457	45273	5.4846%
   reads: 	893620	46289	5.1799%
----------------
Candidate insertion sites in file: EG73N_insert.txt
  reads:	7965
  uqreads:	7836
  Number of Candidate sites:	7836

Level 1 collapse of insertion sites in file: EG73N_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	519

Level 1 annotation file: EG73N_level1siteannotation.xls
Insertion sites in fixed bin:
EG73N_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	EG73N.noGEN.front	EG73N.noGEN.front.gendel	percent
uq reads:	825457	315510	38.2225%
   reads: 	893620	326353	36.5203%
----------------
match_dm6_mask_gen_del:1:
  reads:	EG73N.noGEN.end	EG73N.noGEN.end.gendel	percent
uq reads:	825457	328636	39.8126%
   reads: 	893620	339643	38.0075%
----------------
Candidate breakpoint sites in file: EG73N_depletion.xls
  reads:	23654
  uqreads:	23142
  Number of reads supporting candidate sites:	23142

Level 1 collapse of depletion sites in file: EG73N_depletion_level1.xls
  Number of Level 1 collapsed sites:	2637