Insertion Pipeline
Bowtie2_wholegenome:
  reads:	D8.fastq.uq.polyn	D8.filter	percent
uq reads:	47708023	1984512	4.1597%
   reads: 	58211322	3162339	5.4325%
----------------
virus_structural_rna_repbase_filter:
  reads:	D8.filter	D8.nostrna	percent
uq reads:	1984512	1937438	97.6279%
   reads: 	3162339	3076059	97.2716%
----------------
TE_filter:
  reads:	D8.nostrna	D8.noTE	percent
uq reads:	1937438	1932153	99.7272%
   reads: 	3076059	3070343	99.8142%
----------------
match_dm6_mask_gen:1:
  reads:	D8.noGEN.front	D8.noGEN.front.gen	percent
uq reads:	1932153	651793	33.7340%
   reads: 	3070343	1255215	40.8819%
----------------
match_TE:2:
  reads:	D8.noGEN.front	D8.noGEN.front.TE	percent
uq reads:	1932153	123526	6.3932%
   reads: 	3070343	139091	4.5301%
----------------
match_dm6_mask_gen:1:
  reads:	D8.noGEN.end	D8.noGEN.end.gen	percent
uq reads:	1932153	617177	31.9424%
   reads: 	3070343	1209183	39.3827%
----------------
match_TE:2:
  reads:	D8.noGEN.end	D8.noGEN.end.TE	percent
uq reads:	1932153	119031	6.1605%
   reads: 	3070343	134923	4.3944%
----------------
Candidate insertion sites in file: D8_insert.txt
  reads:	16836
  uqreads:	15468
  Number of Candidate sites:	15468

Level 1 collapse of insertion sites in file: D8_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	929

Level 1 annotation file: D8_level1siteannotation.xls
Insertion sites in fixed bin:
D8_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	D8.noGEN.front	D8.noGEN.front.gendel	percent
uq reads:	1932153	651793	33.7340%
   reads: 	3070343	1255215	40.8819%
----------------
match_dm6_mask_gen_del:1:
  reads:	D8.noGEN.end	D8.noGEN.end.gendel	percent
uq reads:	1932153	617177	31.9424%
   reads: 	3070343	1209183	39.3827%
----------------
Candidate breakpoint sites in file: D8_depletion.xls
  reads:	26890
  uqreads:	24589
  Number of reads supporting candidate sites:	24589

Level 1 collapse of depletion sites in file: D8_depletion_level1.xls
  Number of Level 1 collapsed sites:	2304