Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ISO1-CL-HEm3.fastq.uq.polyn	ISO1-CL-HEm3.filter	percent
uq reads:	15396412	169680	1.1021%
   reads: 	16240857	176132	1.0845%
----------------
virus_structural_rna_repbase_filter:
  reads:	ISO1-CL-HEm3.filter	ISO1-CL-HEm3.nostrna	percent
uq reads:	169680	85864	50.6035%
   reads: 	176132	87760	49.8263%
----------------
TE_filter:
  reads:	ISO1-CL-HEm3.nostrna	ISO1-CL-HEm3.noTE	percent
uq reads:	85864	85607	99.7007%
   reads: 	87760	87500	99.7037%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-CL-HEm3.noGEN.front	ISO1-CL-HEm3.noGEN.front.gen	percent
uq reads:	85607	38328	44.7720%
   reads: 	87500	38548	44.0549%
----------------
match_TE:2:
  reads:	ISO1-CL-HEm3.noGEN.front	ISO1-CL-HEm3.noGEN.front.TE	percent
uq reads:	85607	15897	18.5697%
   reads: 	87500	16303	18.6320%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-CL-HEm3.noGEN.end	ISO1-CL-HEm3.noGEN.end.gen	percent
uq reads:	85607	28206	32.9482%
   reads: 	87500	28402	32.4594%
----------------
match_TE:2:
  reads:	ISO1-CL-HEm3.noGEN.end	ISO1-CL-HEm3.noGEN.end.TE	percent
uq reads:	85607	15011	17.5348%
   reads: 	87500	15446	17.6526%
----------------
Candidate insertion sites in file: ISO1-CL-HEm3_insert.txt
  reads:	2137
  uqreads:	2098
  Number of Candidate sites:	2098

Level 1 collapse of insertion sites in file: ISO1-CL-HEm3_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	115

Level 1 annotation file: ISO1-CL-HEm3_level1siteannotation.xls
Insertion sites in fixed bin:
ISO1-CL-HEm3_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ISO1-CL-HEm3.noGEN.front	ISO1-CL-HEm3.noGEN.front.gendel	percent
uq reads:	85607	38328	44.7720%
   reads: 	87500	38548	44.0549%
----------------
match_dm6_mask_gen_del:1:
  reads:	ISO1-CL-HEm3.noGEN.end	ISO1-CL-HEm3.noGEN.end.gendel	percent
uq reads:	85607	28206	32.9482%
   reads: 	87500	28402	32.4594%
----------------
Candidate breakpoint sites in file: ISO1-CL-HEm3_depletion.xls
  reads:	1853
  uqreads:	1842
  Number of reads supporting candidate sites:	1842

Level 1 collapse of depletion sites in file: ISO1-CL-HEm3_depletion_level1.xls
  Number of Level 1 collapsed sites:	47