Insertion Pipeline
Bowtie2_wholegenome:
  reads:	w[1118].fastq.uq.polyn	w[1118].filter	percent
uq reads:	36358582	811393	2.2316%
   reads: 	39796213	1235656	3.1050%
----------------
virus_structural_rna_repbase_filter:
  reads:	w[1118].filter	w[1118].nostrna	percent
uq reads:	811393	783308	96.5387%
   reads: 	1235656	1044819	84.5558%
----------------
TE_filter:
  reads:	w[1118].nostrna	w[1118].noTE	percent
uq reads:	783308	776163	99.0878%
   reads: 	1044819	1033192	98.8872%
----------------
match_dm6_mask_gen:1:
  reads:	w[1118].noGEN.front	w[1118].noGEN.front.gen	percent
uq reads:	776163	307821	39.6593%
   reads: 	1033192	341525	33.0553%
----------------
match_TE:2:
  reads:	w[1118].noGEN.front	w[1118].noGEN.front.TE	percent
uq reads:	776163	46847	6.0357%
   reads: 	1033192	53382	5.1667%
----------------
match_dm6_mask_gen:1:
  reads:	w[1118].noGEN.end	w[1118].noGEN.end.gen	percent
uq reads:	776163	248085	31.9630%
   reads: 	1033192	282884	27.3796%
----------------
match_TE:2:
  reads:	w[1118].noGEN.end	w[1118].noGEN.end.TE	percent
uq reads:	776163	44933	5.7891%
   reads: 	1033192	52122	5.0448%
----------------
Candidate insertion sites in file: w[1118]_insert.txt
  reads:	16769
  uqreads:	15440
  Number of Candidate sites:	15440

Level 1 collapse of insertion sites in file: w[1118]_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	531

Level 1 annotation file: w[1118]_level1siteannotation.xls
Insertion sites in fixed bin:
w[1118]_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	w[1118].noGEN.front	w[1118].noGEN.front.gendel	percent
uq reads:	776163	307821	39.6593%
   reads: 	1033192	341525	33.0553%
----------------
match_dm6_mask_gen_del:1:
  reads:	w[1118].noGEN.end	w[1118].noGEN.end.gendel	percent
uq reads:	776163	248085	31.9630%
   reads: 	1033192	282884	27.3796%
----------------
Candidate breakpoint sites in file: w[1118]_depletion.xls
  reads:	50382
  uqreads:	46413
  Number of reads supporting candidate sites:	46413

Level 1 collapse of depletion sites in file: w[1118]_depletion_level1.xls
  Number of Level 1 collapsed sites:	2955