Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ISO1-BL.fastq.uq.polyn	ISO1-BL.filter	percent
uq reads:	127246604	6451190	5.0698%
   reads: 	176040655	13931982	7.9141%
----------------
virus_structural_rna_repbase_filter:
  reads:	ISO1-BL.filter	ISO1-BL.nostrna	percent
uq reads:	6451190	3681020	57.0596%
   reads: 	13931982	8544795	61.3322%
----------------
TE_filter:
  reads:	ISO1-BL.nostrna	ISO1-BL.noTE	percent
uq reads:	3681020	3661373	99.4663%
   reads: 	8544795	8514438	99.6447%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-BL.noGEN.front	ISO1-BL.noGEN.front.gen	percent
uq reads:	3661373	786953	21.4934%
   reads: 	8514438	1675623	19.6798%
----------------
match_TE:2:
  reads:	ISO1-BL.noGEN.front	ISO1-BL.noGEN.front.TE	percent
uq reads:	3661373	361503	9.8734%
   reads: 	8514438	553973	6.5063%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-BL.noGEN.end	ISO1-BL.noGEN.end.gen	percent
uq reads:	3661373	680709	18.5916%
   reads: 	8514438	1573528	18.4807%
----------------
match_TE:2:
  reads:	ISO1-BL.noGEN.end	ISO1-BL.noGEN.end.TE	percent
uq reads:	3661373	356780	9.7444%
   reads: 	8514438	559288	6.5687%
----------------
Candidate insertion sites in file: ISO1-BL_insert.txt
  reads:	36429
  uqreads:	28263
  Number of Candidate sites:	28263

Level 1 collapse of insertion sites in file: ISO1-BL_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	239

Level 1 annotation file: ISO1-BL_level1siteannotation.xls
Insertion sites in fixed bin:
ISO1-BL_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ISO1-BL.noGEN.front	ISO1-BL.noGEN.front.gendel	percent
uq reads:	3661373	786953	21.4934%
   reads: 	8514438	1675623	19.6798%
----------------
match_dm6_mask_gen_del:1:
  reads:	ISO1-BL.noGEN.end	ISO1-BL.noGEN.end.gendel	percent
uq reads:	3661373	680709	18.5916%
   reads: 	8514438	1573528	18.4807%
----------------
Candidate breakpoint sites in file: ISO1-BL_depletion.xls
  reads:	12888
  uqreads:	10486
  Number of reads supporting candidate sites:	10486

Level 1 collapse of depletion sites in file: ISO1-BL_depletion_level1.xls
  Number of Level 1 collapsed sites:	293