Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ISO1-CL-HEm12.fastq.uq.polyn	ISO1-CL-HEm12.filter	percent
uq reads:	75928239	1903682	2.5072%
   reads: 	86682538	2059085	2.3754%
----------------
virus_structural_rna_repbase_filter:
  reads:	ISO1-CL-HEm12.filter	ISO1-CL-HEm12.nostrna	percent
uq reads:	1903682	1331035	69.9190%
   reads: 	2059085	1395713	67.7832%
----------------
TE_filter:
  reads:	ISO1-CL-HEm12.nostrna	ISO1-CL-HEm12.noTE	percent
uq reads:	1331035	1329318	99.8710%
   reads: 	1395713	1393924	99.8718%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-CL-HEm12.noGEN.front	ISO1-CL-HEm12.noGEN.front.gen	percent
uq reads:	1329318	284117	21.3731%
   reads: 	1393924	289503	20.7689%
----------------
match_TE:2:
  reads:	ISO1-CL-HEm12.noGEN.front	ISO1-CL-HEm12.noGEN.front.TE	percent
uq reads:	1329318	94729	7.1261%
   reads: 	1393924	104657	7.5081%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-CL-HEm12.noGEN.end	ISO1-CL-HEm12.noGEN.end.gen	percent
uq reads:	1329318	252220	18.9736%
   reads: 	1393924	257280	18.4572%
----------------
match_TE:2:
  reads:	ISO1-CL-HEm12.noGEN.end	ISO1-CL-HEm12.noGEN.end.TE	percent
uq reads:	1329318	93009	6.9967%
   reads: 	1393924	103240	7.4064%
----------------
Candidate insertion sites in file: ISO1-CL-HEm12_insert.txt
  reads:	10159
  uqreads:	9593
  Number of Candidate sites:	9593

Level 1 collapse of insertion sites in file: ISO1-CL-HEm12_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	169

Level 1 annotation file: ISO1-CL-HEm12_level1siteannotation.xls
Insertion sites in fixed bin:
ISO1-CL-HEm12_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ISO1-CL-HEm12.noGEN.front	ISO1-CL-HEm12.noGEN.front.gendel	percent
uq reads:	1329318	284117	21.3731%
   reads: 	1393924	289503	20.7689%
----------------
match_dm6_mask_gen_del:1:
  reads:	ISO1-CL-HEm12.noGEN.end	ISO1-CL-HEm12.noGEN.end.gendel	percent
uq reads:	1329318	252220	18.9736%
   reads: 	1393924	257280	18.4572%
----------------
Candidate breakpoint sites in file: ISO1-CL-HEm12_depletion.xls
  reads:	9941
  uqreads:	9753
  Number of reads supporting candidate sites:	9753

Level 1 collapse of depletion sites in file: ISO1-CL-HEm12_depletion_level1.xls
  Number of Level 1 collapsed sites:	107