Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-382.fastq.uq.polyn	RAL-382.filter	percent
uq reads:	59889825	9585513	16.0052%
   reads: 	72832106	16074585	22.0707%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-382.filter	RAL-382.nostrna	percent
uq reads:	9585513	6193957	64.6179%
   reads: 	16074585	9159052	56.9785%
----------------
TE_filter:
  reads:	RAL-382.nostrna	RAL-382.noTE	percent
uq reads:	6193957	6183616	99.8330%
   reads: 	9159052	9142746	99.8220%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-382.noGEN.front	RAL-382.noGEN.front.gen	percent
uq reads:	6183616	1783485	28.8421%
   reads: 	9142746	2241605	24.5179%
----------------
match_TE:2:
  reads:	RAL-382.noGEN.front	RAL-382.noGEN.front.TE	percent
uq reads:	6183616	277079	4.4809%
   reads: 	9142746	323277	3.5359%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-382.noGEN.end	RAL-382.noGEN.end.gen	percent
uq reads:	6183616	856429	13.8500%
   reads: 	9142746	1301054	14.2305%
----------------
match_TE:2:
  reads:	RAL-382.noGEN.end	RAL-382.noGEN.end.TE	percent
uq reads:	6183616	159611	2.5812%
   reads: 	9142746	205547	2.2482%
----------------
Candidate insertion sites in file: RAL-382_insert.txt
  reads:	33964
  uqreads:	31912
  Number of Candidate sites:	31912

Level 1 collapse of insertion sites in file: RAL-382_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	673

Level 1 annotation file: RAL-382_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-382_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-382.noGEN.front	RAL-382.noGEN.front.gendel	percent
uq reads:	6183616	1783485	28.8421%
   reads: 	9142746	2241605	24.5179%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-382.noGEN.end	RAL-382.noGEN.end.gendel	percent
uq reads:	6183616	856429	13.8500%
   reads: 	9142746	1301054	14.2305%
----------------
Candidate breakpoint sites in file: RAL-382_depletion.xls
  reads:	87676
  uqreads:	81910
  Number of reads supporting candidate sites:	81910

Level 1 collapse of depletion sites in file: RAL-382_depletion_level1.xls
  Number of Level 1 collapsed sites:	4185