Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-461.fastq.uq.polyn	RAL-461.filter	percent
uq reads:	36559560	5826047	15.9358%
   reads: 	42262740	7541346	17.8440%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-461.filter	RAL-461.nostrna	percent
uq reads:	5826047	3019131	51.8213%
   reads: 	7541346	4123843	54.6831%
----------------
TE_filter:
  reads:	RAL-461.nostrna	RAL-461.noTE	percent
uq reads:	3019131	3002022	99.4333%
   reads: 	4123843	4104844	99.5393%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-461.noGEN.front	RAL-461.noGEN.front.gen	percent
uq reads:	3002022	626982	20.8853%
   reads: 	4104844	841680	20.5046%
----------------
match_TE:2:
  reads:	RAL-461.noGEN.front	RAL-461.noGEN.front.TE	percent
uq reads:	3002022	95370	3.1769%
   reads: 	4104844	116709	2.8432%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-461.noGEN.end	RAL-461.noGEN.end.gen	percent
uq reads:	3002022	539515	17.9717%
   reads: 	4104844	755970	18.4165%
----------------
match_TE:2:
  reads:	RAL-461.noGEN.end	RAL-461.noGEN.end.TE	percent
uq reads:	3002022	82736	2.7560%
   reads: 	4104844	103743	2.5273%
----------------
Candidate insertion sites in file: RAL-461_insert.txt
  reads:	12124
  uqreads:	11798
  Number of Candidate sites:	11798

Level 1 collapse of insertion sites in file: RAL-461_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	571

Level 1 annotation file: RAL-461_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-461_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-461.noGEN.front	RAL-461.noGEN.front.gendel	percent
uq reads:	3002022	637675	21.2415%
   reads: 	4104844	859869	20.9477%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-461.noGEN.end	RAL-461.noGEN.end.gendel	percent
uq reads:	3002022	547876	18.2502%
   reads: 	4104844	769171	18.7381%
----------------
Candidate breakpoint sites in file: RAL-461_depletion.xls
  reads:	28866
  uqreads:	28087
  Number of reads supporting candidate sites:	28087

Level 1 collapse of depletion sites in file: RAL-461_depletion_level1.xls
  Number of Level 1 collapsed sites:	2568