Insertion Pipeline
Bowtie2_wholegenome:
  reads:	OSS_C.fastq.uq.polyn	OSS_C.filter	percent
uq reads:	25811064	3263196	12.6426%
   reads: 	29556306	3661185	12.3872%
----------------
virus_structural_rna_repbase_filter:
  reads:	OSS_C.filter	OSS_C.nostrna	percent
uq reads:	3263196	3243299	99.3903%
   reads: 	3661185	3614164	98.7157%
----------------
TE_filter:
  reads:	OSS_C.nostrna	OSS_C.noTE	percent
uq reads:	3243299	3239914	99.8956%
   reads: 	3614164	3610415	99.8963%
----------------
match_dm6_mask_gen:1:
  reads:	OSS_C.noGEN.front	OSS_C.noGEN.front.gen	percent
uq reads:	3239914	1359127	41.9495%
   reads: 	3610415	1386838	38.4121%
----------------
match_TE:2:
  reads:	OSS_C.noGEN.front	OSS_C.noGEN.front.TE	percent
uq reads:	3239914	315887	9.7499%
   reads: 	3610415	323535	8.9612%
----------------
match_dm6_mask_gen:1:
  reads:	OSS_C.noGEN.end	OSS_C.noGEN.end.gen	percent
uq reads:	3239914	251432	7.7605%
   reads: 	3610415	271625	7.5234%
----------------
match_TE:2:
  reads:	OSS_C.noGEN.end	OSS_C.noGEN.end.TE	percent
uq reads:	3239914	108063	3.3354%
   reads: 	3610415	114970	3.1844%
----------------
Candidate insertion sites in file: OSS_C_insert.txt
  reads:	40730
  uqreads:	39733
  Number of Candidate sites:	39733

Level 1 collapse of insertion sites in file: OSS_C_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	2605

Level 1 annotation file: OSS_C_level1siteannotation.xls
Insertion sites in fixed bin:
OSS_C_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	OSS_C.noGEN.front	OSS_C.noGEN.front.gendel	percent
uq reads:	3239914	1359127	41.9495%
   reads: 	3610415	1386838	38.4121%
----------------
match_dm6_mask_gen_del:1:
  reads:	OSS_C.noGEN.end	OSS_C.noGEN.end.gendel	percent
uq reads:	3239914	251432	7.7605%
   reads: 	3610415	271625	7.5234%
----------------
Candidate breakpoint sites in file: OSS_C_depletion.xls
  reads:	33816
  uqreads:	33051
  Number of reads supporting candidate sites:	33051

Level 1 collapse of depletion sites in file: OSS_C_depletion_level1.xls
  Number of Level 1 collapsed sites:	2750