Insertion Pipeline
Bowtie2_wholegenome:
  reads:	Samar-Dw1.fastq.uq.polyn	Samar-Dw1.filter	percent
uq reads:	41089947	2272507	5.5306%
   reads: 	57194170	4297383	7.5137%
----------------
virus_structural_rna_repbase_filter:
  reads:	Samar-Dw1.filter	Samar-Dw1.nostrna	percent
uq reads:	2272507	2253792	99.1765%
   reads: 	4297383	4262007	99.1768%
----------------
TE_filter:
  reads:	Samar-Dw1.nostrna	Samar-Dw1.noTE	percent
uq reads:	2253792	2248395	99.7605%
   reads: 	4262007	4254767	99.8301%
----------------
match_dm6_mask_gen:1:
  reads:	Samar-Dw1.noGEN.front	Samar-Dw1.noGEN.front.gen	percent
uq reads:	2248395	376257	16.7345%
   reads: 	4254767	1219418	28.6600%
----------------
match_TE:2:
  reads:	Samar-Dw1.noGEN.front	Samar-Dw1.noGEN.front.TE	percent
uq reads:	2248395	100697	4.4786%
   reads: 	4254767	132869	3.1228%
----------------
match_dm6_mask_gen:1:
  reads:	Samar-Dw1.noGEN.end	Samar-Dw1.noGEN.end.gen	percent
uq reads:	2248395	340773	15.1563%
   reads: 	4254767	1162019	27.3110%
----------------
match_TE:2:
  reads:	Samar-Dw1.noGEN.end	Samar-Dw1.noGEN.end.TE	percent
uq reads:	2248395	97272	4.3263%
   reads: 	4254767	129022	3.0324%
----------------
Candidate insertion sites in file: Samar-Dw1_insert.txt
  reads:	10773
  uqreads:	9249
  Number of Candidate sites:	9249

Level 1 collapse of insertion sites in file: Samar-Dw1_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	537

Level 1 annotation file: Samar-Dw1_level1siteannotation.xls
Insertion sites in fixed bin:
Samar-Dw1_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	Samar-Dw1.noGEN.front	Samar-Dw1.noGEN.front.gendel	percent
uq reads:	2248395	376257	16.7345%
   reads: 	4254767	1219418	28.6600%
----------------
match_dm6_mask_gen_del:1:
  reads:	Samar-Dw1.noGEN.end	Samar-Dw1.noGEN.end.gendel	percent
uq reads:	2248395	340773	15.1563%
   reads: 	4254767	1162019	27.3110%
----------------
Candidate breakpoint sites in file: Samar-Dw1_depletion.xls
  reads:	22809
  uqreads:	19500
  Number of reads supporting candidate sites:	19500

Level 1 collapse of depletion sites in file: Samar-Dw1_depletion_level1.xls
  Number of Level 1 collapsed sites:	1784