Insertion Pipeline
Bowtie2_wholegenome:
  reads:	SF332_1-HE.fastq.uq.polyn	SF332_1-HE.filter	percent
uq reads:	26222648	1649344	6.2898%
   reads: 	27126844	1681321	6.1980%
----------------
virus_structural_rna_repbase_filter:
  reads:	SF332_1-HE.filter	SF332_1-HE.nostrna	percent
uq reads:	1649344	1418769	86.0202%
   reads: 	1681321	1441375	85.7287%
----------------
TE_filter:
  reads:	SF332_1-HE.nostrna	SF332_1-HE.noTE	percent
uq reads:	1418769	1414117	99.6721%
   reads: 	1441375	1435849	99.6166%
----------------
match_dm6_mask_gen:1:
  reads:	SF332_1-HE.noGEN.front	SF332_1-HE.noGEN.front.gen	percent
uq reads:	1414117	797534	56.3980%
   reads: 	1435849	806405	56.1622%
----------------
match_TE:2:
  reads:	SF332_1-HE.noGEN.front	SF332_1-HE.noGEN.front.TE	percent
uq reads:	1414117	71981	5.0902%
   reads: 	1435849	73198	5.0979%
----------------
match_dm6_mask_gen:1:
  reads:	SF332_1-HE.noGEN.end	SF332_1-HE.noGEN.end.gen	percent
uq reads:	1414117	796630	56.3341%
   reads: 	1435849	806065	56.1386%
----------------
match_TE:2:
  reads:	SF332_1-HE.noGEN.end	SF332_1-HE.noGEN.end.TE	percent
uq reads:	1414117	72763	5.1455%
   reads: 	1435849	73999	5.1537%
----------------
Candidate insertion sites in file: SF332_1-HE_insert.txt
  reads:	15760
  uqreads:	15465
  Number of Candidate sites:	15465

Level 1 collapse of insertion sites in file: SF332_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	472

Level 1 annotation file: SF332_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
SF332_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	SF332_1-HE.noGEN.front	SF332_1-HE.noGEN.front.gendel	percent
uq reads:	1414117	797534	56.3980%
   reads: 	1435849	806405	56.1622%
----------------
match_dm6_mask_gen_del:1:
  reads:	SF332_1-HE.noGEN.end	SF332_1-HE.noGEN.end.gendel	percent
uq reads:	1414117	796630	56.3341%
   reads: 	1435849	806065	56.1386%
----------------
Candidate breakpoint sites in file: SF332_1-HE_depletion.xls
  reads:	66496
  uqreads:	65517
  Number of reads supporting candidate sites:	65517

Level 1 collapse of depletion sites in file: SF332_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3153