Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ISO1-CL1.fastq.uq.polyn	ISO1-CL1.filter	percent
uq reads:	40973537	1648677	4.0238%
   reads: 	43200955	2014159	4.6623%
----------------
virus_structural_rna_repbase_filter:
  reads:	ISO1-CL1.filter	ISO1-CL1.nostrna	percent
uq reads:	1648677	1299581	78.8257%
   reads: 	2014159	1652664	82.0523%
----------------
TE_filter:
  reads:	ISO1-CL1.nostrna	ISO1-CL1.noTE	percent
uq reads:	1299581	1293237	99.5118%
   reads: 	1652664	1646236	99.6111%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-CL1.noGEN.front	ISO1-CL1.noGEN.front.gen	percent
uq reads:	1293237	337903	26.1285%
   reads: 	1646236	579823	35.2211%
----------------
match_TE:2:
  reads:	ISO1-CL1.noGEN.front	ISO1-CL1.noGEN.front.TE	percent
uq reads:	1293237	65016	5.0274%
   reads: 	1646236	65860	4.0006%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-CL1.noGEN.end	ISO1-CL1.noGEN.end.gen	percent
uq reads:	1293237	205320	15.8764%
   reads: 	1646236	425025	25.8180%
----------------
match_TE:2:
  reads:	ISO1-CL1.noGEN.end	ISO1-CL1.noGEN.end.TE	percent
uq reads:	1293237	59456	4.5975%
   reads: 	1646236	61349	3.7266%
----------------
Candidate insertion sites in file: ISO1-CL1_insert.txt
  reads:	2794
  uqreads:	2745
  Number of Candidate sites:	2745

Level 1 collapse of insertion sites in file: ISO1-CL1_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	92

Level 1 annotation file: ISO1-CL1_level1siteannotation.xls
Insertion sites in fixed bin:
ISO1-CL1_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ISO1-CL1.noGEN.front	ISO1-CL1.noGEN.front.gendel	percent
uq reads:	1293237	337903	26.1285%
   reads: 	1646236	579823	35.2211%
----------------
match_dm6_mask_gen_del:1:
  reads:	ISO1-CL1.noGEN.end	ISO1-CL1.noGEN.end.gendel	percent
uq reads:	1293237	205320	15.8764%
   reads: 	1646236	425025	25.8180%
----------------
Candidate breakpoint sites in file: ISO1-CL1_depletion.xls
  reads:	2434
  uqreads:	1753
  Number of reads supporting candidate sites:	1753

Level 1 collapse of depletion sites in file: ISO1-CL1_depletion_level1.xls
  Number of Level 1 collapsed sites:	78