Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-409_95b.fastq.uq.polyn	RAL-409_95b.filter	percent
uq reads:	30314503	4501510	14.8494%
   reads: 	31454024	4702008	14.9488%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-409_95b.filter	RAL-409_95b.nostrna	percent
uq reads:	4501510	2488380	55.2788%
   reads: 	4702008	2623439	55.7940%
----------------
TE_filter:
  reads:	RAL-409_95b.nostrna	RAL-409_95b.noTE	percent
uq reads:	2488380	2479643	99.6489%
   reads: 	2623439	2614541	99.6608%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-409_95b.noGEN.front	RAL-409_95b.noGEN.front.gen	percent
uq reads:	2479643	801600	32.3272%
   reads: 	2614541	883559	33.7940%
----------------
match_TE:2:
  reads:	RAL-409_95b.noGEN.front	RAL-409_95b.noGEN.front.TE	percent
uq reads:	2479643	101095	4.0770%
   reads: 	2614541	101964	3.8999%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-409_95b.noGEN.end	RAL-409_95b.noGEN.end.gen	percent
uq reads:	2479643	612208	24.6894%
   reads: 	2614541	688452	26.3317%
----------------
match_TE:2:
  reads:	RAL-409_95b.noGEN.end	RAL-409_95b.noGEN.end.TE	percent
uq reads:	2479643	83964	3.3861%
   reads: 	2614541	85178	3.2579%
----------------
Candidate insertion sites in file: RAL-409_95b_insert.txt
  reads:	7433
  uqreads:	7416
  Number of Candidate sites:	7416

Level 1 collapse of insertion sites in file: RAL-409_95b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	452

Level 1 annotation file: RAL-409_95b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-409_95b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-409_95b.noGEN.front	RAL-409_95b.noGEN.front.gendel	percent
uq reads:	2479643	801600	32.3272%
   reads: 	2614541	883559	33.7940%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-409_95b.noGEN.end	RAL-409_95b.noGEN.end.gendel	percent
uq reads:	2479643	612208	24.6894%
   reads: 	2614541	688452	26.3317%
----------------
Candidate breakpoint sites in file: RAL-409_95b_depletion.xls
  reads:	16861
  uqreads:	16789
  Number of reads supporting candidate sites:	16789

Level 1 collapse of depletion sites in file: RAL-409_95b_depletion_level1.xls
  Number of Level 1 collapsed sites:	1463