Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-38.fastq.uq.polyn	RAL-38.filter	percent
uq reads:	48090505	3282485	6.8256%
   reads: 	54967537	4768665	8.6754%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-38.filter	RAL-38.nostrna	percent
uq reads:	3282485	3174955	96.7241%
   reads: 	4768665	4437877	93.0633%
----------------
TE_filter:
  reads:	RAL-38.nostrna	RAL-38.noTE	percent
uq reads:	3174955	3159483	99.5127%
   reads: 	4437877	4417364	99.5378%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-38.noGEN.front	RAL-38.noGEN.front.gen	percent
uq reads:	3159483	990096	31.3373%
   reads: 	4417364	1267050	28.6834%
----------------
match_TE:2:
  reads:	RAL-38.noGEN.front	RAL-38.noGEN.front.TE	percent
uq reads:	3159483	164995	5.2222%
   reads: 	4417364	188999	4.2785%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-38.noGEN.end	RAL-38.noGEN.end.gen	percent
uq reads:	3159483	910492	28.8178%
   reads: 	4417364	1183688	26.7963%
----------------
match_TE:2:
  reads:	RAL-38.noGEN.end	RAL-38.noGEN.end.TE	percent
uq reads:	3159483	161131	5.0999%
   reads: 	4417364	186828	4.2294%
----------------
Candidate insertion sites in file: RAL-38_insert.txt
  reads:	29107
  uqreads:	28214
  Number of Candidate sites:	28214

Level 1 collapse of insertion sites in file: RAL-38_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	782

Level 1 annotation file: RAL-38_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-38_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-38.noGEN.front	RAL-38.noGEN.front.gendel	percent
uq reads:	3159483	1008650	31.9245%
   reads: 	4417364	1288692	29.1733%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-38.noGEN.end	RAL-38.noGEN.end.gendel	percent
uq reads:	3159483	927262	29.3485%
   reads: 	4417364	1202948	27.2323%
----------------
Candidate breakpoint sites in file: RAL-38_depletion.xls
  reads:	65540
  uqreads:	62737
  Number of reads supporting candidate sites:	62737

Level 1 collapse of depletion sites in file: RAL-38_depletion_level1.xls
  Number of Level 1 collapsed sites:	3578