Insertion Pipeline
Bowtie2_wholegenome:
  reads:	SP80_1-HE.fastq.uq.polyn	SP80_1-HE.filter	percent
uq reads:	34799427	1428158	4.1040%
   reads: 	36053423	1466501	4.0676%
----------------
virus_structural_rna_repbase_filter:
  reads:	SP80_1-HE.filter	SP80_1-HE.nostrna	percent
uq reads:	1428158	1289511	90.2919%
   reads: 	1466501	1322182	90.1590%
----------------
TE_filter:
  reads:	SP80_1-HE.nostrna	SP80_1-HE.noTE	percent
uq reads:	1289511	1284396	99.6033%
   reads: 	1322182	1315786	99.5163%
----------------
match_dm6_mask_gen:1:
  reads:	SP80_1-HE.noGEN.front	SP80_1-HE.noGEN.front.gen	percent
uq reads:	1284396	777269	60.5163%
   reads: 	1315786	790773	60.0989%
----------------
match_TE:2:
  reads:	SP80_1-HE.noGEN.front	SP80_1-HE.noGEN.front.TE	percent
uq reads:	1284396	78171	6.0862%
   reads: 	1315786	79742	6.0604%
----------------
match_dm6_mask_gen:1:
  reads:	SP80_1-HE.noGEN.end	SP80_1-HE.noGEN.end.gen	percent
uq reads:	1284396	618355	48.1436%
   reads: 	1315786	632327	48.0570%
----------------
match_TE:2:
  reads:	SP80_1-HE.noGEN.end	SP80_1-HE.noGEN.end.TE	percent
uq reads:	1284396	68156	5.3065%
   reads: 	1315786	69691	5.2965%
----------------
Candidate insertion sites in file: SP80_1-HE_insert.txt
  reads:	21896
  uqreads:	21184
  Number of Candidate sites:	21184

Level 1 collapse of insertion sites in file: SP80_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	516

Level 1 annotation file: SP80_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
SP80_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	SP80_1-HE.noGEN.front	SP80_1-HE.noGEN.front.gendel	percent
uq reads:	1284396	777269	60.5163%
   reads: 	1315786	790773	60.0989%
----------------
match_dm6_mask_gen_del:1:
  reads:	SP80_1-HE.noGEN.end	SP80_1-HE.noGEN.end.gendel	percent
uq reads:	1284396	618355	48.1436%
   reads: 	1315786	632327	48.0570%
----------------
Candidate breakpoint sites in file: SP80_1-HE_depletion.xls
  reads:	89894
  uqreads:	87077
  Number of reads supporting candidate sites:	87077

Level 1 collapse of depletion sites in file: SP80_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	4333