Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-837.fastq.uq.polyn	RAL-837.filter	percent
uq reads:	41841301	6813103	16.2832%
   reads: 	45377733	8345113	18.3903%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-837.filter	RAL-837.nostrna	percent
uq reads:	6813103	2673963	39.2474%
   reads: 	8345113	3157706	37.8390%
----------------
TE_filter:
  reads:	RAL-837.nostrna	RAL-837.noTE	percent
uq reads:	2673963	2659744	99.4682%
   reads: 	3157706	3141907	99.4997%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-837.noGEN.front	RAL-837.noGEN.front.gen	percent
uq reads:	2659744	709398	26.6717%
   reads: 	3141907	803075	25.5601%
----------------
match_TE:2:
  reads:	RAL-837.noGEN.front	RAL-837.noGEN.front.TE	percent
uq reads:	2659744	100003	3.7599%
   reads: 	3141907	109176	3.4748%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-837.noGEN.end	RAL-837.noGEN.end.gen	percent
uq reads:	2659744	551281	20.7268%
   reads: 	3141907	646898	20.5893%
----------------
match_TE:2:
  reads:	RAL-837.noGEN.end	RAL-837.noGEN.end.TE	percent
uq reads:	2659744	85870	3.2285%
   reads: 	3141907	95517	3.0401%
----------------
Candidate insertion sites in file: RAL-837_insert.txt
  reads:	12454
  uqreads:	12302
  Number of Candidate sites:	12302

Level 1 collapse of insertion sites in file: RAL-837_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	589

Level 1 annotation file: RAL-837_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-837_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-837.noGEN.front	RAL-837.noGEN.front.gendel	percent
uq reads:	2659744	719488	27.0510%
   reads: 	3141907	816436	25.9854%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-837.noGEN.end	RAL-837.noGEN.end.gendel	percent
uq reads:	2659744	559422	21.0329%
   reads: 	3141907	657132	20.9151%
----------------
Candidate breakpoint sites in file: RAL-837_depletion.xls
  reads:	31929
  uqreads:	31460
  Number of reads supporting candidate sites:	31460

Level 1 collapse of depletion sites in file: RAL-837_depletion_level1.xls
  Number of Level 1 collapsed sites:	2967