Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-589.fastq.uq.polyn	RAL-589.filter	percent
uq reads:	27707237	2764497	9.9775%
   reads: 	32701256	3826928	11.7027%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-589.filter	RAL-589.nostrna	percent
uq reads:	2764497	1652404	59.7723%
   reads: 	3826928	1946633	50.8667%
----------------
TE_filter:
  reads:	RAL-589.nostrna	RAL-589.noTE	percent
uq reads:	1652404	1643363	99.4529%
   reads: 	1946633	1934517	99.3776%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-589.noGEN.front	RAL-589.noGEN.front.gen	percent
uq reads:	1643363	437394	26.6158%
   reads: 	1934517	576907	29.8218%
----------------
match_TE:2:
  reads:	RAL-589.noGEN.front	RAL-589.noGEN.front.TE	percent
uq reads:	1643363	56299	3.4258%
   reads: 	1934517	61630	3.1858%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-589.noGEN.end	RAL-589.noGEN.end.gen	percent
uq reads:	1643363	473561	28.8166%
   reads: 	1934517	599095	30.9687%
----------------
match_TE:2:
  reads:	RAL-589.noGEN.end	RAL-589.noGEN.end.TE	percent
uq reads:	1643363	61104	3.7182%
   reads: 	1934517	66709	3.4484%
----------------
Candidate insertion sites in file: RAL-589_insert.txt
  reads:	5515
  uqreads:	4892
  Number of Candidate sites:	4892

Level 1 collapse of insertion sites in file: RAL-589_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	324

Level 1 annotation file: RAL-589_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-589_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-589.noGEN.front	RAL-589.noGEN.front.gendel	percent
uq reads:	1643363	444037	27.0200%
   reads: 	1934517	587037	30.3454%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-589.noGEN.end	RAL-589.noGEN.end.gendel	percent
uq reads:	1643363	480128	29.2162%
   reads: 	1934517	608879	31.4745%
----------------
Candidate breakpoint sites in file: RAL-589_depletion.xls
  reads:	13472
  uqreads:	11566
  Number of reads supporting candidate sites:	11566

Level 1 collapse of depletion sites in file: RAL-589_depletion_level1.xls
  Number of Level 1 collapsed sites:	1072