Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-57.fastq.uq.polyn	RAL-57.filter	percent
uq reads:	57730475	6518980	11.2921%
   reads: 	63910169	8071930	12.6301%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-57.filter	RAL-57.nostrna	percent
uq reads:	6518980	6429005	98.6198%
   reads: 	8071930	7928660	98.2251%
----------------
TE_filter:
  reads:	RAL-57.nostrna	RAL-57.noTE	percent
uq reads:	6429005	6386788	99.3433%
   reads: 	7928660	7880835	99.3968%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-57.noGEN.front	RAL-57.noGEN.front.gen	percent
uq reads:	6386788	2788875	43.6663%
   reads: 	7880835	3383446	42.9326%
----------------
match_TE:2:
  reads:	RAL-57.noGEN.front	RAL-57.noGEN.front.TE	percent
uq reads:	6386788	437201	6.8454%
   reads: 	7880835	454253	5.7640%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-57.noGEN.end	RAL-57.noGEN.end.gen	percent
uq reads:	6386788	2469646	38.6680%
   reads: 	7880835	3068066	38.9307%
----------------
match_TE:2:
  reads:	RAL-57.noGEN.end	RAL-57.noGEN.end.TE	percent
uq reads:	6386788	432801	6.7765%
   reads: 	7880835	453535	5.7549%
----------------
Candidate insertion sites in file: RAL-57_insert.txt
  reads:	71121
  uqreads:	70400
  Number of Candidate sites:	70400

Level 1 collapse of insertion sites in file: RAL-57_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	653

Level 1 annotation file: RAL-57_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-57_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-57.noGEN.front	RAL-57.noGEN.front.gendel	percent
uq reads:	6386788	2788875	43.6663%
   reads: 	7880835	3383446	42.9326%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-57.noGEN.end	RAL-57.noGEN.end.gendel	percent
uq reads:	6386788	2469646	38.6680%
   reads: 	7880835	3068066	38.9307%
----------------
Candidate breakpoint sites in file: RAL-57_depletion.xls
  reads:	148805
  uqreads:	145651
  Number of reads supporting candidate sites:	145651

Level 1 collapse of depletion sites in file: RAL-57_depletion_level1.xls
  Number of Level 1 collapsed sites:	2699