Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-371_125b.fastq.uq.polyn	RAL-371_125b.filter	percent
uq reads:	24537774	1948760	7.9419%
   reads: 	26901539	2528924	9.4007%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-371_125b.filter	RAL-371_125b.nostrna	percent
uq reads:	1948760	1919380	98.4924%
   reads: 	2528924	2444365	96.6563%
----------------
TE_filter:
  reads:	RAL-371_125b.nostrna	RAL-371_125b.noTE	percent
uq reads:	1919380	1912343	99.6334%
   reads: 	2444365	2435928	99.6548%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-371_125b.noGEN.front	RAL-371_125b.noGEN.front.gen	percent
uq reads:	1912343	820263	42.8931%
   reads: 	2435928	977315	40.1208%
----------------
match_TE:2:
  reads:	RAL-371_125b.noGEN.front	RAL-371_125b.noGEN.front.TE	percent
uq reads:	1912343	135923	7.1077%
   reads: 	2435928	144757	5.9426%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-371_125b.noGEN.end	RAL-371_125b.noGEN.end.gen	percent
uq reads:	1912343	303576	15.8746%
   reads: 	2435928	452151	18.5618%
----------------
match_TE:2:
  reads:	RAL-371_125b.noGEN.end	RAL-371_125b.noGEN.end.TE	percent
uq reads:	1912343	65991	3.4508%
   reads: 	2435928	74696	3.0664%
----------------
Candidate insertion sites in file: RAL-371_125b_insert.txt
  reads:	13071
  uqreads:	12732
  Number of Candidate sites:	12732

Level 1 collapse of insertion sites in file: RAL-371_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	530

Level 1 annotation file: RAL-371_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-371_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-371_125b.noGEN.front	RAL-371_125b.noGEN.front.gendel	percent
uq reads:	1912343	820263	42.8931%
   reads: 	2435928	977315	40.1208%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-371_125b.noGEN.end	RAL-371_125b.noGEN.end.gendel	percent
uq reads:	1912343	303576	15.8746%
   reads: 	2435928	452151	18.5618%
----------------
Candidate breakpoint sites in file: RAL-371_125b_depletion.xls
  reads:	35484
  uqreads:	34444
  Number of reads supporting candidate sites:	34444

Level 1 collapse of depletion sites in file: RAL-371_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3010