Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-584_125b.fastq.uq.polyn	RAL-584_125b.filter	percent
uq reads:	41694160	7312770	17.5391%
   reads: 	45261269	8722181	19.2707%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-584_125b.filter	RAL-584_125b.nostrna	percent
uq reads:	7312770	4433282	60.6238%
   reads: 	8722181	5024943	57.6111%
----------------
TE_filter:
  reads:	RAL-584_125b.nostrna	RAL-584_125b.noTE	percent
uq reads:	4433282	4413635	99.5568%
   reads: 	5024943	5002959	99.5625%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-584_125b.noGEN.front	RAL-584_125b.noGEN.front.gen	percent
uq reads:	4413635	1161602	26.3185%
   reads: 	5002959	1337555	26.7353%
----------------
match_TE:2:
  reads:	RAL-584_125b.noGEN.front	RAL-584_125b.noGEN.front.TE	percent
uq reads:	4413635	191460	4.3379%
   reads: 	5002959	200561	4.0088%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-584_125b.noGEN.end	RAL-584_125b.noGEN.end.gen	percent
uq reads:	4413635	515183	11.6725%
   reads: 	5002959	682356	13.6390%
----------------
match_TE:2:
  reads:	RAL-584_125b.noGEN.end	RAL-584_125b.noGEN.end.TE	percent
uq reads:	4413635	104231	2.3616%
   reads: 	5002959	113173	2.2621%
----------------
Candidate insertion sites in file: RAL-584_125b_insert.txt
  reads:	20076
  uqreads:	19740
  Number of Candidate sites:	19740

Level 1 collapse of insertion sites in file: RAL-584_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	585

Level 1 annotation file: RAL-584_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-584_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-584_125b.noGEN.front	RAL-584_125b.noGEN.front.gendel	percent
uq reads:	4413635	1161602	26.3185%
   reads: 	5002959	1337555	26.7353%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-584_125b.noGEN.end	RAL-584_125b.noGEN.end.gendel	percent
uq reads:	4413635	515183	11.6725%
   reads: 	5002959	682356	13.6390%
----------------
Candidate breakpoint sites in file: RAL-584_125b_depletion.xls
  reads:	53691
  uqreads:	52520
  Number of reads supporting candidate sites:	52520

Level 1 collapse of depletion sites in file: RAL-584_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3674