Insertion Pipeline
Bowtie2_wholegenome:
  reads:	OreR-SE.fastq.uq.polyn	OreR-SE.filter	percent
uq reads:	47815644	3355048	7.0166%
   reads: 	54605553	4281084	7.8400%
----------------
virus_structural_rna_repbase_filter:
  reads:	OreR-SE.filter	OreR-SE.nostrna	percent
uq reads:	3355048	3323360	99.0555%
   reads: 	4281084	4133339	96.5489%
----------------
TE_filter:
  reads:	OreR-SE.nostrna	OreR-SE.noTE	percent
uq reads:	3323360	3305446	99.4610%
   reads: 	4133339	4075928	98.6110%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-SE.noGEN.front	OreR-SE.noGEN.front.gen	percent
uq reads:	3305446	1274967	38.5717%
   reads: 	4075928	1408878	34.5658%
----------------
match_TE:2:
  reads:	OreR-SE.noGEN.front	OreR-SE.noGEN.front.TE	percent
uq reads:	3305446	197309	5.9692%
   reads: 	4075928	210307	5.1597%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-SE.noGEN.end	OreR-SE.noGEN.end.gen	percent
uq reads:	3305446	440130	13.3153%
   reads: 	4075928	549032	13.4701%
----------------
match_TE:2:
  reads:	OreR-SE.noGEN.end	OreR-SE.noGEN.end.TE	percent
uq reads:	3305446	126872	3.8383%
   reads: 	4075928	141340	3.4677%
----------------
Candidate insertion sites in file: OreR-SE_insert.txt
  reads:	37358
  uqreads:	35461
  Number of Candidate sites:	35461

Level 1 collapse of insertion sites in file: OreR-SE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1213

Level 1 annotation file: OreR-SE_level1siteannotation.xls
Insertion sites in fixed bin:
OreR-SE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	OreR-SE.noGEN.front	OreR-SE.noGEN.front.gendel	percent
uq reads:	3305446	1274967	38.5717%
   reads: 	4075928	1408878	34.5658%
----------------
match_dm6_mask_gen_del:1:
  reads:	OreR-SE.noGEN.end	OreR-SE.noGEN.end.gendel	percent
uq reads:	3305446	440130	13.3153%
   reads: 	4075928	549032	13.4701%
----------------
Candidate breakpoint sites in file: OreR-SE_depletion.xls
  reads:	69173
  uqreads:	63506
  Number of reads supporting candidate sites:	63506

Level 1 collapse of depletion sites in file: OreR-SE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3803