Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-371_75b.fastq.uq.polyn	RAL-371_75b.filter	percent
uq reads:	76796688	7010691	9.1289%
   reads: 	84199989	8419042	9.9989%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-371_75b.filter	RAL-371_75b.nostrna	percent
uq reads:	7010691	6843191	97.6108%
   reads: 	8419042	8113416	96.3698%
----------------
TE_filter:
  reads:	RAL-371_75b.nostrna	RAL-371_75b.noTE	percent
uq reads:	6843191	6816609	99.6116%
   reads: 	8113416	8082606	99.6203%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-371_75b.noGEN.front	RAL-371_75b.noGEN.front.gen	percent
uq reads:	6816609	2698793	39.5914%
   reads: 	8082606	3201016	39.6038%
----------------
match_TE:2:
  reads:	RAL-371_75b.noGEN.front	RAL-371_75b.noGEN.front.TE	percent
uq reads:	6816609	386642	5.6721%
   reads: 	8082606	409902	5.0714%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-371_75b.noGEN.end	RAL-371_75b.noGEN.end.gen	percent
uq reads:	6816609	1562120	22.9164%
   reads: 	8082606	2039880	25.2379%
----------------
match_TE:2:
  reads:	RAL-371_75b.noGEN.end	RAL-371_75b.noGEN.end.TE	percent
uq reads:	6816609	262669	3.8534%
   reads: 	8082606	286227	3.5413%
----------------
Candidate insertion sites in file: RAL-371_75b_insert.txt
  reads:	36536
  uqreads:	35736
  Number of Candidate sites:	35736

Level 1 collapse of insertion sites in file: RAL-371_75b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	652

Level 1 annotation file: RAL-371_75b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-371_75b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-371_75b.noGEN.front	RAL-371_75b.noGEN.front.gendel	percent
uq reads:	6816609	2698793	39.5914%
   reads: 	8082606	3201016	39.6038%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-371_75b.noGEN.end	RAL-371_75b.noGEN.end.gendel	percent
uq reads:	6816609	1562120	22.9164%
   reads: 	8082606	2039880	25.2379%
----------------
Candidate breakpoint sites in file: RAL-371_75b_depletion.xls
  reads:	88141
  uqreads:	85744
  Number of reads supporting candidate sites:	85744

Level 1 collapse of depletion sites in file: RAL-371_75b_depletion_level1.xls
  Number of Level 1 collapsed sites:	4891