Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-373_125b.fastq.uq.polyn	RAL-373_125b.filter	percent
uq reads:	42262645	5018338	11.8742%
   reads: 	44835082	5714885	12.7465%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-373_125b.filter	RAL-373_125b.nostrna	percent
uq reads:	5018338	4920321	98.0468%
   reads: 	5714885	5534400	96.8418%
----------------
TE_filter:
  reads:	RAL-373_125b.nostrna	RAL-373_125b.noTE	percent
uq reads:	4920321	4909739	99.7849%
   reads: 	5534400	5522708	99.7887%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-373_125b.noGEN.front	RAL-373_125b.noGEN.front.gen	percent
uq reads:	4909739	2250489	45.8372%
   reads: 	5522708	2430714	44.0131%
----------------
match_TE:2:
  reads:	RAL-373_125b.noGEN.front	RAL-373_125b.noGEN.front.TE	percent
uq reads:	4909739	338965	6.9039%
   reads: 	5522708	350041	6.3382%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-373_125b.noGEN.end	RAL-373_125b.noGEN.end.gen	percent
uq reads:	4909739	815599	16.6119%
   reads: 	5522708	981719	17.7760%
----------------
match_TE:2:
  reads:	RAL-373_125b.noGEN.end	RAL-373_125b.noGEN.end.TE	percent
uq reads:	4909739	150984	3.0752%
   reads: 	5522708	161740	2.9286%
----------------
Candidate insertion sites in file: RAL-373_125b_insert.txt
  reads:	32565
  uqreads:	32190
  Number of Candidate sites:	32190

Level 1 collapse of insertion sites in file: RAL-373_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	712

Level 1 annotation file: RAL-373_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-373_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-373_125b.noGEN.front	RAL-373_125b.noGEN.front.gendel	percent
uq reads:	4909739	2250489	45.8372%
   reads: 	5522708	2430714	44.0131%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-373_125b.noGEN.end	RAL-373_125b.noGEN.end.gendel	percent
uq reads:	4909739	815599	16.6119%
   reads: 	5522708	981719	17.7760%
----------------
Candidate breakpoint sites in file: RAL-373_125b_depletion.xls
  reads:	75226
  uqreads:	74080
  Number of reads supporting candidate sites:	74080

Level 1 collapse of depletion sites in file: RAL-373_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3937