Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ZS11_1-HE.fastq.uq.polyn	ZS11_1-HE.filter	percent
uq reads:	55607998	3255911	5.8551%
   reads: 	63938281	3797330	5.9391%
----------------
virus_structural_rna_repbase_filter:
  reads:	ZS11_1-HE.filter	ZS11_1-HE.nostrna	percent
uq reads:	3255911	2346510	72.0692%
   reads: 	3797330	2593254	68.2915%
----------------
TE_filter:
  reads:	ZS11_1-HE.nostrna	ZS11_1-HE.noTE	percent
uq reads:	2346510	2334087	99.4706%
   reads: 	2593254	2569533	99.0853%
----------------
match_dm6_mask_gen:1:
  reads:	ZS11_1-HE.noGEN.front	ZS11_1-HE.noGEN.front.gen	percent
uq reads:	2334087	1158664	49.6410%
   reads: 	2569533	1270967	49.4630%
----------------
match_TE:2:
  reads:	ZS11_1-HE.noGEN.front	ZS11_1-HE.noGEN.front.TE	percent
uq reads:	2334087	81747	3.5023%
   reads: 	2569533	89095	3.4674%
----------------
match_dm6_mask_gen:1:
  reads:	ZS11_1-HE.noGEN.end	ZS11_1-HE.noGEN.end.gen	percent
uq reads:	2334087	1190342	50.9982%
   reads: 	2569533	1315439	51.1937%
----------------
match_TE:2:
  reads:	ZS11_1-HE.noGEN.end	ZS11_1-HE.noGEN.end.TE	percent
uq reads:	2334087	81115	3.4752%
   reads: 	2569533	88369	3.4391%
----------------
Candidate insertion sites in file: ZS11_1-HE_insert.txt
  reads:	17626
  uqreads:	15722
  Number of Candidate sites:	15722

Level 1 collapse of insertion sites in file: ZS11_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	509

Level 1 annotation file: ZS11_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
ZS11_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ZS11_1-HE.noGEN.front	ZS11_1-HE.noGEN.front.gendel	percent
uq reads:	2334087	1158664	49.6410%
   reads: 	2569533	1270967	49.4630%
----------------
match_dm6_mask_gen_del:1:
  reads:	ZS11_1-HE.noGEN.end	ZS11_1-HE.noGEN.end.gendel	percent
uq reads:	2334087	1190342	50.9982%
   reads: 	2569533	1315439	51.1937%
----------------
Candidate breakpoint sites in file: ZS11_1-HE_depletion.xls
  reads:	63931
  uqreads:	56988
  Number of reads supporting candidate sites:	56988

Level 1 collapse of depletion sites in file: ZS11_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3571