Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-307_75b.fastq.uq.polyn	RAL-307_75b.filter	percent
uq reads:	9998733	775438	7.7554%
   reads: 	12772053	958951	7.5082%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-307_75b.filter	RAL-307_75b.nostrna	percent
uq reads:	775438	753515	97.1728%
   reads: 	958951	917690	95.6973%
----------------
TE_filter:
  reads:	RAL-307_75b.nostrna	RAL-307_75b.noTE	percent
uq reads:	753515	749030	99.4048%
   reads: 	917690	911803	99.3585%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-307_75b.noGEN.front	RAL-307_75b.noGEN.front.gen	percent
uq reads:	749030	314923	42.0441%
   reads: 	911803	366984	40.2482%
----------------
match_TE:2:
  reads:	RAL-307_75b.noGEN.front	RAL-307_75b.noGEN.front.TE	percent
uq reads:	749030	40786	5.4452%
   reads: 	911803	46553	5.1056%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-307_75b.noGEN.end	RAL-307_75b.noGEN.end.gen	percent
uq reads:	749030	149712	19.9875%
   reads: 	911803	200972	22.0412%
----------------
match_TE:2:
  reads:	RAL-307_75b.noGEN.end	RAL-307_75b.noGEN.end.TE	percent
uq reads:	749030	27213	3.6331%
   reads: 	911803	32927	3.6112%
----------------
Candidate insertion sites in file: RAL-307_75b_insert.txt
  reads:	3455
  uqreads:	2801
  Number of Candidate sites:	2801

Level 1 collapse of insertion sites in file: RAL-307_75b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	178

Level 1 annotation file: RAL-307_75b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-307_75b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-307_75b.noGEN.front	RAL-307_75b.noGEN.front.gendel	percent
uq reads:	749030	314923	42.0441%
   reads: 	911803	366984	40.2482%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-307_75b.noGEN.end	RAL-307_75b.noGEN.end.gendel	percent
uq reads:	749030	149712	19.9875%
   reads: 	911803	200972	22.0412%
----------------
Candidate breakpoint sites in file: RAL-307_75b_depletion.xls
  reads:	8200
  uqreads:	6296
  Number of reads supporting candidate sites:	6296

Level 1 collapse of depletion sites in file: RAL-307_75b_depletion_level1.xls
  Number of Level 1 collapsed sites:	480