Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-821_125b.fastq.uq.polyn	RAL-821_125b.filter	percent
uq reads:	72354902	11264189	15.5680%
   reads: 	82773683	15517944	18.7474%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-821_125b.filter	RAL-821_125b.nostrna	percent
uq reads:	11264189	7353435	65.2815%
   reads: 	15517944	8627959	55.5999%
----------------
TE_filter:
  reads:	RAL-821_125b.nostrna	RAL-821_125b.noTE	percent
uq reads:	7353435	7337716	99.7862%
   reads: 	8627959	8604278	99.7255%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-821_125b.noGEN.front	RAL-821_125b.noGEN.front.gen	percent
uq reads:	7337716	1529755	20.8478%
   reads: 	8604278	1860490	21.6228%
----------------
match_TE:2:
  reads:	RAL-821_125b.noGEN.front	RAL-821_125b.noGEN.front.TE	percent
uq reads:	7337716	269462	3.6723%
   reads: 	8604278	289416	3.3636%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-821_125b.noGEN.end	RAL-821_125b.noGEN.end.gen	percent
uq reads:	7337716	906170	12.3495%
   reads: 	8604278	1225296	14.2405%
----------------
match_TE:2:
  reads:	RAL-821_125b.noGEN.end	RAL-821_125b.noGEN.end.TE	percent
uq reads:	7337716	189502	2.5826%
   reads: 	8604278	208690	2.4254%
----------------
Candidate insertion sites in file: RAL-821_125b_insert.txt
  reads:	35066
  uqreads:	33736
  Number of Candidate sites:	33736

Level 1 collapse of insertion sites in file: RAL-821_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	727

Level 1 annotation file: RAL-821_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-821_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-821_125b.noGEN.front	RAL-821_125b.noGEN.front.gendel	percent
uq reads:	7337716	1529755	20.8478%
   reads: 	8604278	1860490	21.6228%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-821_125b.noGEN.end	RAL-821_125b.noGEN.end.gendel	percent
uq reads:	7337716	906170	12.3495%
   reads: 	8604278	1225296	14.2405%
----------------
Candidate breakpoint sites in file: RAL-821_125b_depletion.xls
  reads:	97012
  uqreads:	92490
  Number of reads supporting candidate sites:	92490

Level 1 collapse of depletion sites in file: RAL-821_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	4664