Insertion Pipeline
Bowtie2_wholegenome:
  reads:	GU6_1-HE.fastq.uq.polyn	GU6_1-HE.filter	percent
uq reads:	57606171	2384871	4.1400%
   reads: 	65397414	2664938	4.0750%
----------------
virus_structural_rna_repbase_filter:
  reads:	GU6_1-HE.filter	GU6_1-HE.nostrna	percent
uq reads:	2384871	2360082	98.9606%
   reads: 	2664938	2617881	98.2342%
----------------
TE_filter:
  reads:	GU6_1-HE.nostrna	GU6_1-HE.noTE	percent
uq reads:	2360082	2349252	99.5411%
   reads: 	2617881	2597384	99.2170%
----------------
match_dm6_mask_gen:1:
  reads:	GU6_1-HE.noGEN.front	GU6_1-HE.noGEN.front.gen	percent
uq reads:	2349252	1156875	49.2444%
   reads: 	2597384	1255168	48.3243%
----------------
match_TE:2:
  reads:	GU6_1-HE.noGEN.front	GU6_1-HE.noGEN.front.TE	percent
uq reads:	2349252	91826	3.9087%
   reads: 	2597384	100073	3.8528%
----------------
match_dm6_mask_gen:1:
  reads:	GU6_1-HE.noGEN.end	GU6_1-HE.noGEN.end.gen	percent
uq reads:	2349252	1193799	50.8161%
   reads: 	2597384	1301898	50.1234%
----------------
match_TE:2:
  reads:	GU6_1-HE.noGEN.end	GU6_1-HE.noGEN.end.TE	percent
uq reads:	2349252	91335	3.8878%
   reads: 	2597384	99212	3.8197%
----------------
Candidate insertion sites in file: GU6_1-HE_insert.txt
  reads:	16780
  uqreads:	15187
  Number of Candidate sites:	15187

Level 1 collapse of insertion sites in file: GU6_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	495

Level 1 annotation file: GU6_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
GU6_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	GU6_1-HE.noGEN.front	GU6_1-HE.noGEN.front.gendel	percent
uq reads:	2349252	1156875	49.2444%
   reads: 	2597384	1255168	48.3243%
----------------
match_dm6_mask_gen_del:1:
  reads:	GU6_1-HE.noGEN.end	GU6_1-HE.noGEN.end.gendel	percent
uq reads:	2349252	1193799	50.8161%
   reads: 	2597384	1301898	50.1234%
----------------
Candidate breakpoint sites in file: GU6_1-HE_depletion.xls
  reads:	67242
  uqreads:	60873
  Number of reads supporting candidate sites:	60873

Level 1 collapse of depletion sites in file: GU6_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3886