Insertion Pipeline
Bowtie2_wholegenome:
  reads:	EA119_1-HE.fastq.uq.polyn	EA119_1-HE.filter	percent
uq reads:	30196160	1432843	4.7451%
   reads: 	32718978	1519754	4.6449%
----------------
virus_structural_rna_repbase_filter:
  reads:	EA119_1-HE.filter	EA119_1-HE.nostrna	percent
uq reads:	1432843	1411042	98.4785%
   reads: 	1519754	1477190	97.1993%
----------------
TE_filter:
  reads:	EA119_1-HE.nostrna	EA119_1-HE.noTE	percent
uq reads:	1411042	1406622	99.6868%
   reads: 	1477190	1470123	99.5216%
----------------
match_dm6_mask_gen:1:
  reads:	EA119_1-HE.noGEN.front	EA119_1-HE.noGEN.front.gen	percent
uq reads:	1406622	806768	57.3550%
   reads: 	1470123	827697	56.3012%
----------------
match_TE:2:
  reads:	EA119_1-HE.noGEN.front	EA119_1-HE.noGEN.front.TE	percent
uq reads:	1406622	73800	5.2466%
   reads: 	1470123	76794	5.2236%
----------------
match_dm6_mask_gen:1:
  reads:	EA119_1-HE.noGEN.end	EA119_1-HE.noGEN.end.gen	percent
uq reads:	1406622	768779	54.6543%
   reads: 	1470123	790658	53.7818%
----------------
match_TE:2:
  reads:	EA119_1-HE.noGEN.end	EA119_1-HE.noGEN.end.TE	percent
uq reads:	1406622	71599	5.0901%
   reads: 	1470123	74631	5.0765%
----------------
Candidate insertion sites in file: EA119_1-HE_insert.txt
  reads:	18684
  uqreads:	17974
  Number of Candidate sites:	17974

Level 1 collapse of insertion sites in file: EA119_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	559

Level 1 annotation file: EA119_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
EA119_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	EA119_1-HE.noGEN.front	EA119_1-HE.noGEN.front.gendel	percent
uq reads:	1406622	806768	57.3550%
   reads: 	1470123	827697	56.3012%
----------------
match_dm6_mask_gen_del:1:
  reads:	EA119_1-HE.noGEN.end	EA119_1-HE.noGEN.end.gendel	percent
uq reads:	1406622	768779	54.6543%
   reads: 	1470123	790658	53.7818%
----------------
Candidate breakpoint sites in file: EA119_1-HE_depletion.xls
  reads:	72824
  uqreads:	70353
  Number of reads supporting candidate sites:	70353

Level 1 collapse of depletion sites in file: EA119_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3681