Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-859.fastq.uq.polyn	RAL-859.filter	percent
uq reads:	33837772	4090612	12.0889%
   reads: 	36128381	4560931	12.6242%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-859.filter	RAL-859.nostrna	percent
uq reads:	4090612	3200068	78.2296%
   reads: 	4560931	3563896	78.1397%
----------------
TE_filter:
  reads:	RAL-859.nostrna	RAL-859.noTE	percent
uq reads:	3200068	3186439	99.5741%
   reads: 	3563896	3546956	99.5247%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-859.noGEN.front	RAL-859.noGEN.front.gen	percent
uq reads:	3186439	1451324	45.5469%
   reads: 	3546956	1668059	47.0279%
----------------
match_TE:2:
  reads:	RAL-859.noGEN.front	RAL-859.noGEN.front.TE	percent
uq reads:	3186439	196573	6.1690%
   reads: 	3546956	201133	5.6706%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-859.noGEN.end	RAL-859.noGEN.end.gen	percent
uq reads:	3186439	437265	13.7227%
   reads: 	3546956	626824	17.6722%
----------------
match_TE:2:
  reads:	RAL-859.noGEN.end	RAL-859.noGEN.end.TE	percent
uq reads:	3186439	90253	2.8324%
   reads: 	3546956	96236	2.7132%
----------------
Candidate insertion sites in file: RAL-859_insert.txt
  reads:	8251
  uqreads:	8021
  Number of Candidate sites:	8021

Level 1 collapse of insertion sites in file: RAL-859_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	450

Level 1 annotation file: RAL-859_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-859_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-859.noGEN.front	RAL-859.noGEN.front.gendel	percent
uq reads:	3186439	1451324	45.5469%
   reads: 	3546956	1668059	47.0279%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-859.noGEN.end	RAL-859.noGEN.end.gendel	percent
uq reads:	3186439	437265	13.7227%
   reads: 	3546956	626824	17.6722%
----------------
Candidate breakpoint sites in file: RAL-859_depletion.xls
  reads:	18328
  uqreads:	17339
  Number of reads supporting candidate sites:	17339

Level 1 collapse of depletion sites in file: RAL-859_depletion_level1.xls
  Number of Level 1 collapsed sites:	1830