Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-189.fastq.uq.polyn	RAL-189.filter	percent
uq reads:	54944954	6089486	11.0829%
   reads: 	61416874	7447508	12.1262%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-189.filter	RAL-189.nostrna	percent
uq reads:	6089486	4629468	76.0240%
   reads: 	7447508	5459585	73.3075%
----------------
TE_filter:
  reads:	RAL-189.nostrna	RAL-189.noTE	percent
uq reads:	4629468	4618658	99.7665%
   reads: 	5459585	5442280	99.6830%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-189.noGEN.front	RAL-189.noGEN.front.gen	percent
uq reads:	4618658	1535596	33.2477%
   reads: 	5442280	1870563	34.3709%
----------------
match_TE:2:
  reads:	RAL-189.noGEN.front	RAL-189.noGEN.front.TE	percent
uq reads:	4618658	245647	5.3186%
   reads: 	5442280	261090	4.7974%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-189.noGEN.end	RAL-189.noGEN.end.gen	percent
uq reads:	4618658	701410	15.1864%
   reads: 	5442280	1036533	19.0459%
----------------
match_TE:2:
  reads:	RAL-189.noGEN.end	RAL-189.noGEN.end.TE	percent
uq reads:	4618658	148154	3.2077%
   reads: 	5442280	163300	3.0006%
----------------
Candidate insertion sites in file: RAL-189_insert.txt
  reads:	29265
  uqreads:	27881
  Number of Candidate sites:	27881

Level 1 collapse of insertion sites in file: RAL-189_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	629

Level 1 annotation file: RAL-189_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-189_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-189.noGEN.front	RAL-189.noGEN.front.gendel	percent
uq reads:	4618658	1535596	33.2477%
   reads: 	5442280	1870563	34.3709%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-189.noGEN.end	RAL-189.noGEN.end.gendel	percent
uq reads:	4618658	701410	15.1864%
   reads: 	5442280	1036533	19.0459%
----------------
Candidate breakpoint sites in file: RAL-189_depletion.xls
  reads:	82656
  uqreads:	77940
  Number of reads supporting candidate sites:	77940

Level 1 collapse of depletion sites in file: RAL-189_depletion_level1.xls
  Number of Level 1 collapsed sites:	4269