Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-894.fastq.uq.polyn	RAL-894.filter	percent
uq reads:	32040570	2683470	8.3752%
   reads: 	34467384	3424990	9.9369%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-894.filter	RAL-894.nostrna	percent
uq reads:	2683470	2481365	92.4685%
   reads: 	3424990	2960750	86.4455%
----------------
TE_filter:
  reads:	RAL-894.nostrna	RAL-894.noTE	percent
uq reads:	2481365	2468057	99.4637%
   reads: 	2960750	2945956	99.5003%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-894.noGEN.front	RAL-894.noGEN.front.gen	percent
uq reads:	2468057	722722	29.2830%
   reads: 	2945956	799540	27.1403%
----------------
match_TE:2:
  reads:	RAL-894.noGEN.front	RAL-894.noGEN.front.TE	percent
uq reads:	2468057	101154	4.0985%
   reads: 	2945956	108821	3.6939%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-894.noGEN.end	RAL-894.noGEN.end.gen	percent
uq reads:	2468057	630171	25.5331%
   reads: 	2945956	703824	23.8912%
----------------
match_TE:2:
  reads:	RAL-894.noGEN.end	RAL-894.noGEN.end.TE	percent
uq reads:	2468057	99753	4.0418%
   reads: 	2945956	108718	3.6904%
----------------
Candidate insertion sites in file: RAL-894_insert.txt
  reads:	17620
  uqreads:	17313
  Number of Candidate sites:	17313

Level 1 collapse of insertion sites in file: RAL-894_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	603

Level 1 annotation file: RAL-894_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-894_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-894.noGEN.front	RAL-894.noGEN.front.gendel	percent
uq reads:	2468057	735956	29.8192%
   reads: 	2945956	814667	27.6537%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-894.noGEN.end	RAL-894.noGEN.end.gendel	percent
uq reads:	2468057	642055	26.0146%
   reads: 	2945956	717411	24.3524%
----------------
Candidate breakpoint sites in file: RAL-894_depletion.xls
  reads:	34045
  uqreads:	33311
  Number of reads supporting candidate sites:	33311

Level 1 collapse of depletion sites in file: RAL-894_depletion_level1.xls
  Number of Level 1 collapsed sites:	2523