Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-705.fastq.uq.polyn	RAL-705.filter	percent
uq reads:	42716090	9374160	21.9453%
   reads: 	45400582	10063724	22.1665%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-705.filter	RAL-705.nostrna	percent
uq reads:	9374160	8388145	89.4816%
   reads: 	10063724	8951975	88.9529%
----------------
TE_filter:
  reads:	RAL-705.nostrna	RAL-705.noTE	percent
uq reads:	8388145	8377053	99.8678%
   reads: 	8951975	8939306	99.8585%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-705.noGEN.front	RAL-705.noGEN.front.gen	percent
uq reads:	8377053	3001406	35.8289%
   reads: 	8939306	3248566	36.3402%
----------------
match_TE:2:
  reads:	RAL-705.noGEN.front	RAL-705.noGEN.front.TE	percent
uq reads:	8377053	391695	4.6758%
   reads: 	8939306	395466	4.4239%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-705.noGEN.end	RAL-705.noGEN.end.gen	percent
uq reads:	8377053	706507	8.4338%
   reads: 	8939306	929454	10.3974%
----------------
match_TE:2:
  reads:	RAL-705.noGEN.end	RAL-705.noGEN.end.TE	percent
uq reads:	8377053	149185	1.7809%
   reads: 	8939306	154191	1.7249%
----------------
Candidate insertion sites in file: RAL-705_insert.txt
  reads:	10972
  uqreads:	10749
  Number of Candidate sites:	10749

Level 1 collapse of insertion sites in file: RAL-705_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	494

Level 1 annotation file: RAL-705_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-705_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-705.noGEN.front	RAL-705.noGEN.front.gendel	percent
uq reads:	8377053	3001406	35.8289%
   reads: 	8939306	3248566	36.3402%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-705.noGEN.end	RAL-705.noGEN.end.gendel	percent
uq reads:	8377053	706507	8.4338%
   reads: 	8939306	929454	10.3974%
----------------
Candidate breakpoint sites in file: RAL-705_depletion.xls
  reads:	21547
  uqreads:	20018
  Number of reads supporting candidate sites:	20018

Level 1 collapse of depletion sites in file: RAL-705_depletion_level1.xls
  Number of Level 1 collapsed sites:	2009