Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-45.fastq.uq.polyn	RAL-45.filter	percent
uq reads:	34037235	3548236	10.4246%
   reads: 	36027558	3926150	10.8976%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-45.filter	RAL-45.nostrna	percent
uq reads:	3548236	3494266	98.4790%
   reads: 	3926150	3870222	98.5755%
----------------
TE_filter:
  reads:	RAL-45.nostrna	RAL-45.noTE	percent
uq reads:	3494266	3484441	99.7188%
   reads: 	3870222	3858060	99.6858%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-45.noGEN.front	RAL-45.noGEN.front.gen	percent
uq reads:	3484441	438173	12.5751%
   reads: 	3858060	648812	16.8171%
----------------
match_TE:2:
  reads:	RAL-45.noGEN.front	RAL-45.noGEN.front.TE	percent
uq reads:	3484441	66485	1.9081%
   reads: 	3858060	68724	1.7813%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-45.noGEN.end	RAL-45.noGEN.end.gen	percent
uq reads:	3484441	431944	12.3964%
   reads: 	3858060	647177	16.7747%
----------------
match_TE:2:
  reads:	RAL-45.noGEN.end	RAL-45.noGEN.end.TE	percent
uq reads:	3484441	71961	2.0652%
   reads: 	3858060	74313	1.9262%
----------------
Candidate insertion sites in file: RAL-45_insert.txt
  reads:	5868
  uqreads:	5746
  Number of Candidate sites:	5746

Level 1 collapse of insertion sites in file: RAL-45_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	416

Level 1 annotation file: RAL-45_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-45_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-45.noGEN.front	RAL-45.noGEN.front.gendel	percent
uq reads:	3484441	438173	12.5751%
   reads: 	3858060	648812	16.8171%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-45.noGEN.end	RAL-45.noGEN.end.gendel	percent
uq reads:	3484441	431944	12.3964%
   reads: 	3858060	647177	16.7747%
----------------
Candidate breakpoint sites in file: RAL-45_depletion.xls
  reads:	14947
  uqreads:	14494
  Number of reads supporting candidate sites:	14494

Level 1 collapse of depletion sites in file: RAL-45_depletion_level1.xls
  Number of Level 1 collapsed sites:	1448