Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-911.fastq.uq.polyn	RAL-911.filter	percent
uq reads:	30056333	3459039	11.5085%
   reads: 	32190339	4114983	12.7833%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-911.filter	RAL-911.nostrna	percent
uq reads:	3459039	3273363	94.6322%
   reads: 	4114983	3710871	90.1795%
----------------
TE_filter:
  reads:	RAL-911.nostrna	RAL-911.noTE	percent
uq reads:	3273363	3258545	99.5473%
   reads: 	3710871	3695208	99.5779%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-911.noGEN.front	RAL-911.noGEN.front.gen	percent
uq reads:	3258545	1332498	40.8924%
   reads: 	3695208	1413056	38.2402%
----------------
match_TE:2:
  reads:	RAL-911.noGEN.front	RAL-911.noGEN.front.TE	percent
uq reads:	3258545	174872	5.3666%
   reads: 	3695208	182514	4.9392%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-911.noGEN.end	RAL-911.noGEN.end.gen	percent
uq reads:	3258545	557186	17.0992%
   reads: 	3695208	631437	17.0880%
----------------
match_TE:2:
  reads:	RAL-911.noGEN.end	RAL-911.noGEN.end.TE	percent
uq reads:	3258545	137832	4.2299%
   reads: 	3695208	147326	3.9869%
----------------
Candidate insertion sites in file: RAL-911_insert.txt
  reads:	16003
  uqreads:	15842
  Number of Candidate sites:	15842

Level 1 collapse of insertion sites in file: RAL-911_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	499

Level 1 annotation file: RAL-911_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-911_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-911.noGEN.front	RAL-911.noGEN.front.gendel	percent
uq reads:	3258545	1354427	41.5654%
   reads: 	3695208	1435995	38.8610%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-911.noGEN.end	RAL-911.noGEN.end.gendel	percent
uq reads:	3258545	575766	17.6694%
   reads: 	3695208	651129	17.6209%
----------------
Candidate breakpoint sites in file: RAL-911_depletion.xls
  reads:	25853
  uqreads:	25303
  Number of reads supporting candidate sites:	25303

Level 1 collapse of depletion sites in file: RAL-911_depletion_level1.xls
  Number of Level 1 collapsed sites:	2075