Insertion Pipeline
Bowtie2_wholegenome:
  reads:	OreR-AS-FC.fastq.uq.polyn	OreR-AS-FC.filter	percent
uq reads:	68547445	3087293	4.5039%
   reads: 	85174920	3615410	4.2447%
----------------
virus_structural_rna_repbase_filter:
  reads:	OreR-AS-FC.filter	OreR-AS-FC.nostrna	percent
uq reads:	3087293	3064480	99.2611%
   reads: 	3615410	3544233	98.0313%
----------------
TE_filter:
  reads:	OreR-AS-FC.nostrna	OreR-AS-FC.noTE	percent
uq reads:	3064480	3059792	99.8470%
   reads: 	3544233	3537072	99.7980%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-AS-FC.noGEN.front	OreR-AS-FC.noGEN.front.gen	percent
uq reads:	3059792	2032310	66.4199%
   reads: 	3537072	2301661	65.0725%
----------------
match_TE:2:
  reads:	OreR-AS-FC.noGEN.front	OreR-AS-FC.noGEN.front.TE	percent
uq reads:	3059792	155359	5.0774%
   reads: 	3537072	166223	4.6995%
----------------
match_dm6_mask_gen:1:
  reads:	OreR-AS-FC.noGEN.end	OreR-AS-FC.noGEN.end.gen	percent
uq reads:	3059792	426943	13.9533%
   reads: 	3537072	697568	19.7216%
----------------
match_TE:2:
  reads:	OreR-AS-FC.noGEN.end	OreR-AS-FC.noGEN.end.TE	percent
uq reads:	3059792	69685	2.2774%
   reads: 	3537072	81152	2.2943%
----------------
Candidate insertion sites in file: OreR-AS-FC_insert.txt
  reads:	27312
  uqreads:	23848
  Number of Candidate sites:	23848

Level 1 collapse of insertion sites in file: OreR-AS-FC_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	1032

Level 1 annotation file: OreR-AS-FC_level1siteannotation.xls
Insertion sites in fixed bin:
OreR-AS-FC_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	OreR-AS-FC.noGEN.front	OreR-AS-FC.noGEN.front.gendel	percent
uq reads:	3059792	2032310	66.4199%
   reads: 	3537072	2301661	65.0725%
----------------
match_dm6_mask_gen_del:1:
  reads:	OreR-AS-FC.noGEN.end	OreR-AS-FC.noGEN.end.gendel	percent
uq reads:	3059792	426943	13.9533%
   reads: 	3537072	697568	19.7216%
----------------
Candidate breakpoint sites in file: OreR-AS-FC_depletion.xls
  reads:	64401
  uqreads:	53451
  Number of reads supporting candidate sites:	53451

Level 1 collapse of depletion sites in file: OreR-AS-FC_depletion_level1.xls
  Number of Level 1 collapsed sites:	3368