Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-531.fastq.uq.polyn	RAL-531.filter	percent
uq reads:	37080630	6521389	17.5871%
   reads: 	40810121	8070471	19.7757%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-531.filter	RAL-531.nostrna	percent
uq reads:	6521389	3060065	46.9235%
   reads: 	8070471	3568064	44.2113%
----------------
TE_filter:
  reads:	RAL-531.nostrna	RAL-531.noTE	percent
uq reads:	3060065	3049044	99.6398%
   reads: 	3568064	3555290	99.6420%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-531.noGEN.front	RAL-531.noGEN.front.gen	percent
uq reads:	3049044	903583	29.6350%
   reads: 	3555290	991802	27.8965%
----------------
match_TE:2:
  reads:	RAL-531.noGEN.front	RAL-531.noGEN.front.TE	percent
uq reads:	3049044	133982	4.3942%
   reads: 	3555290	145617	4.0958%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-531.noGEN.end	RAL-531.noGEN.end.gen	percent
uq reads:	3049044	640845	21.0179%
   reads: 	3555290	720561	20.2673%
----------------
match_TE:2:
  reads:	RAL-531.noGEN.end	RAL-531.noGEN.end.TE	percent
uq reads:	3049044	116579	3.8235%
   reads: 	3555290	130144	3.6606%
----------------
Candidate insertion sites in file: RAL-531_insert.txt
  reads:	15084
  uqreads:	14721
  Number of Candidate sites:	14721

Level 1 collapse of insertion sites in file: RAL-531_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	574

Level 1 annotation file: RAL-531_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-531_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-531.noGEN.front	RAL-531.noGEN.front.gendel	percent
uq reads:	3049044	919579	30.1596%
   reads: 	3555290	1009557	28.3959%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-531.noGEN.end	RAL-531.noGEN.end.gendel	percent
uq reads:	3049044	653955	21.4479%
   reads: 	3555290	735595	20.6902%
----------------
Candidate breakpoint sites in file: RAL-531_depletion.xls
  reads:	32221
  uqreads:	31271
  Number of reads supporting candidate sites:	31271

Level 1 collapse of depletion sites in file: RAL-531_depletion_level1.xls
  Number of Level 1 collapsed sites:	2598