Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-313.fastq.uq.polyn	RAL-313.filter	percent
uq reads:	11937872	1223492	10.2488%
   reads: 	13877090	1421303	10.2421%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-313.filter	RAL-313.nostrna	percent
uq reads:	1223492	1205292	98.5125%
   reads: 	1421303	1392969	98.0065%
----------------
TE_filter:
  reads:	RAL-313.nostrna	RAL-313.noTE	percent
uq reads:	1205292	1202127	99.7374%
   reads: 	1392969	1389130	99.7244%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-313.noGEN.front	RAL-313.noGEN.front.gen	percent
uq reads:	1202127	502609	41.8100%
   reads: 	1389130	594126	42.7696%
----------------
match_TE:2:
  reads:	RAL-313.noGEN.front	RAL-313.noGEN.front.TE	percent
uq reads:	1202127	72995	6.0722%
   reads: 	1389130	77643	5.5893%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-313.noGEN.end	RAL-313.noGEN.end.gen	percent
uq reads:	1202127	180751	15.0359%
   reads: 	1389130	271635	19.5543%
----------------
match_TE:2:
  reads:	RAL-313.noGEN.end	RAL-313.noGEN.end.TE	percent
uq reads:	1202127	37190	3.0937%
   reads: 	1389130	41958	3.0205%
----------------
Candidate insertion sites in file: RAL-313_insert.txt
  reads:	3649
  uqreads:	3287
  Number of Candidate sites:	3287

Level 1 collapse of insertion sites in file: RAL-313_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	216

Level 1 annotation file: RAL-313_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-313_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-313.noGEN.front	RAL-313.noGEN.front.gendel	percent
uq reads:	1202127	502609	41.8100%
   reads: 	1389130	594126	42.7696%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-313.noGEN.end	RAL-313.noGEN.end.gendel	percent
uq reads:	1202127	180751	15.0359%
   reads: 	1389130	271635	19.5543%
----------------
Candidate breakpoint sites in file: RAL-313_depletion.xls
  reads:	7696
  uqreads:	6667
  Number of reads supporting candidate sites:	6667

Level 1 collapse of depletion sites in file: RAL-313_depletion_level1.xls
  Number of Level 1 collapsed sites:	476