Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-808_125b.fastq.uq.polyn	RAL-808_125b.filter	percent
uq reads:	57610538	8083452	14.0312%
   reads: 	61185648	8905190	14.5544%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-808_125b.filter	RAL-808_125b.nostrna	percent
uq reads:	8083452	7950773	98.3586%
   reads: 	8905190	8594210	96.5079%
----------------
TE_filter:
  reads:	RAL-808_125b.nostrna	RAL-808_125b.noTE	percent
uq reads:	7950773	7938402	99.8444%
   reads: 	8594210	8580702	99.8428%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-808_125b.noGEN.front	RAL-808_125b.noGEN.front.gen	percent
uq reads:	7938402	3150482	39.6866%
   reads: 	8580702	3272147	38.1338%
----------------
match_TE:2:
  reads:	RAL-808_125b.noGEN.front	RAL-808_125b.noGEN.front.TE	percent
uq reads:	7938402	449515	5.6625%
   reads: 	8580702	459248	5.3521%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-808_125b.noGEN.end	RAL-808_125b.noGEN.end.gen	percent
uq reads:	7938402	591002	7.4448%
   reads: 	8580702	703733	8.2013%
----------------
match_TE:2:
  reads:	RAL-808_125b.noGEN.end	RAL-808_125b.noGEN.end.TE	percent
uq reads:	7938402	130669	1.6460%
   reads: 	8580702	139644	1.6274%
----------------
Candidate insertion sites in file: RAL-808_125b_insert.txt
  reads:	25018
  uqreads:	24586
  Number of Candidate sites:	24586

Level 1 collapse of insertion sites in file: RAL-808_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	666

Level 1 annotation file: RAL-808_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-808_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-808_125b.noGEN.front	RAL-808_125b.noGEN.front.gendel	percent
uq reads:	7938402	3150482	39.6866%
   reads: 	8580702	3272147	38.1338%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-808_125b.noGEN.end	RAL-808_125b.noGEN.end.gendel	percent
uq reads:	7938402	591002	7.4448%
   reads: 	8580702	703733	8.2013%
----------------
Candidate breakpoint sites in file: RAL-808_125b_depletion.xls
  reads:	65458
  uqreads:	64027
  Number of reads supporting candidate sites:	64027

Level 1 collapse of depletion sites in file: RAL-808_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3973