Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-900_125b.fastq.uq.polyn	RAL-900_125b.filter	percent
uq reads:	55391102	3853351	6.9566%
   reads: 	64076344	5684093	8.8708%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-900_125b.filter	RAL-900_125b.nostrna	percent
uq reads:	3853351	3769917	97.8348%
   reads: 	5684093	5303691	93.3076%
----------------
TE_filter:
  reads:	RAL-900_125b.nostrna	RAL-900_125b.noTE	percent
uq reads:	3769917	3757660	99.6749%
   reads: 	5303691	5282541	99.6012%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-900_125b.noGEN.front	RAL-900_125b.noGEN.front.gen	percent
uq reads:	3757660	903411	24.0419%
   reads: 	5282541	1285303	24.3312%
----------------
match_TE:2:
  reads:	RAL-900_125b.noGEN.front	RAL-900_125b.noGEN.front.TE	percent
uq reads:	3757660	174553	4.6453%
   reads: 	5282541	211273	3.9995%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-900_125b.noGEN.end	RAL-900_125b.noGEN.end.gen	percent
uq reads:	3757660	640423	17.0431%
   reads: 	5282541	1017675	19.2649%
----------------
match_TE:2:
  reads:	RAL-900_125b.noGEN.end	RAL-900_125b.noGEN.end.TE	percent
uq reads:	3757660	141106	3.7552%
   reads: 	5282541	176179	3.3351%
----------------
Candidate insertion sites in file: RAL-900_125b_insert.txt
  reads:	31555
  uqreads:	29399
  Number of Candidate sites:	29399

Level 1 collapse of insertion sites in file: RAL-900_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	705

Level 1 annotation file: RAL-900_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-900_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-900_125b.noGEN.front	RAL-900_125b.noGEN.front.gendel	percent
uq reads:	3757660	903411	24.0419%
   reads: 	5282541	1285303	24.3312%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-900_125b.noGEN.end	RAL-900_125b.noGEN.end.gendel	percent
uq reads:	3757660	640423	17.0431%
   reads: 	5282541	1017675	19.2649%
----------------
Candidate breakpoint sites in file: RAL-900_125b_depletion.xls
  reads:	88572
  uqreads:	81892
  Number of reads supporting candidate sites:	81892

Level 1 collapse of depletion sites in file: RAL-900_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	4301