Insertion Pipeline
Bowtie2_wholegenome:
  reads:	EF39_1-HE.fastq.uq.polyn	EF39_1-HE.filter	percent
uq reads:	32303989	1547730	4.7911%
   reads: 	34885936	1623622	4.6541%
----------------
virus_structural_rna_repbase_filter:
  reads:	EF39_1-HE.filter	EF39_1-HE.nostrna	percent
uq reads:	1547730	1486710	96.0575%
   reads: 	1623622	1550987	95.5264%
----------------
TE_filter:
  reads:	EF39_1-HE.nostrna	EF39_1-HE.noTE	percent
uq reads:	1486710	1484024	99.8193%
   reads: 	1550987	1547561	99.7791%
----------------
match_dm6_mask_gen:1:
  reads:	EF39_1-HE.noGEN.front	EF39_1-HE.noGEN.front.gen	percent
uq reads:	1484024	848658	57.1863%
   reads: 	1547561	869716	56.1991%
----------------
match_TE:2:
  reads:	EF39_1-HE.noGEN.front	EF39_1-HE.noGEN.front.TE	percent
uq reads:	1484024	103298	6.9607%
   reads: 	1547561	107847	6.9688%
----------------
match_dm6_mask_gen:1:
  reads:	EF39_1-HE.noGEN.end	EF39_1-HE.noGEN.end.gen	percent
uq reads:	1484024	772013	52.0216%
   reads: 	1547561	794072	51.3112%
----------------
match_TE:2:
  reads:	EF39_1-HE.noGEN.end	EF39_1-HE.noGEN.end.TE	percent
uq reads:	1484024	96440	6.4985%
   reads: 	1547561	101056	6.5300%
----------------
Candidate insertion sites in file: EF39_1-HE_insert.txt
  reads:	23770
  uqreads:	22840
  Number of Candidate sites:	22840

Level 1 collapse of insertion sites in file: EF39_1-HE_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	686

Level 1 annotation file: EF39_1-HE_level1siteannotation.xls
Insertion sites in fixed bin:
EF39_1-HE_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	EF39_1-HE.noGEN.front	EF39_1-HE.noGEN.front.gendel	percent
uq reads:	1484024	848658	57.1863%
   reads: 	1547561	869716	56.1991%
----------------
match_dm6_mask_gen_del:1:
  reads:	EF39_1-HE.noGEN.end	EF39_1-HE.noGEN.end.gendel	percent
uq reads:	1484024	772013	52.0216%
   reads: 	1547561	794072	51.3112%
----------------
Candidate breakpoint sites in file: EF39_1-HE_depletion.xls
  reads:	74820
  uqreads:	72004
  Number of reads supporting candidate sites:	72004

Level 1 collapse of depletion sites in file: EF39_1-HE_depletion_level1.xls
  Number of Level 1 collapsed sites:	3904