Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-517.fastq.uq.polyn	RAL-517.filter	percent
uq reads:	40642592	4300887	10.5822%
   reads: 	43280758	4832077	11.1645%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-517.filter	RAL-517.nostrna	percent
uq reads:	4300887	4237968	98.5371%
   reads: 	4832077	4750549	98.3128%
----------------
TE_filter:
  reads:	RAL-517.nostrna	RAL-517.noTE	percent
uq reads:	4237968	4224352	99.6787%
   reads: 	4750549	4735305	99.6791%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-517.noGEN.front	RAL-517.noGEN.front.gen	percent
uq reads:	4224352	2066987	48.9303%
   reads: 	4735305	2393425	50.5443%
----------------
match_TE:2:
  reads:	RAL-517.noGEN.front	RAL-517.noGEN.front.TE	percent
uq reads:	4224352	307402	7.2769%
   reads: 	4735305	312512	6.5996%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-517.noGEN.end	RAL-517.noGEN.end.gen	percent
uq reads:	4224352	714012	16.9023%
   reads: 	4735305	1022805	21.5996%
----------------
match_TE:2:
  reads:	RAL-517.noGEN.end	RAL-517.noGEN.end.TE	percent
uq reads:	4224352	140475	3.3254%
   reads: 	4735305	146822	3.1006%
----------------
Candidate insertion sites in file: RAL-517_insert.txt
  reads:	12539
  uqreads:	12320
  Number of Candidate sites:	12320

Level 1 collapse of insertion sites in file: RAL-517_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	485

Level 1 annotation file: RAL-517_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-517_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-517.noGEN.front	RAL-517.noGEN.front.gendel	percent
uq reads:	4224352	2066987	48.9303%
   reads: 	4735305	2393425	50.5443%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-517.noGEN.end	RAL-517.noGEN.end.gendel	percent
uq reads:	4224352	714012	16.9023%
   reads: 	4735305	1022805	21.5996%
----------------
Candidate breakpoint sites in file: RAL-517_depletion.xls
  reads:	24825
  uqreads:	23637
  Number of reads supporting candidate sites:	23637

Level 1 collapse of depletion sites in file: RAL-517_depletion_level1.xls
  Number of Level 1 collapsed sites:	1943