Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-502.fastq.uq.polyn	RAL-502.filter	percent
uq reads:	41866879	3072584	7.3389%
   reads: 	43621433	3413067	7.8243%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-502.filter	RAL-502.nostrna	percent
uq reads:	3072584	2987359	97.2263%
   reads: 	3413067	3307714	96.9132%
----------------
TE_filter:
  reads:	RAL-502.nostrna	RAL-502.noTE	percent
uq reads:	2987359	2971859	99.4811%
   reads: 	3307714	3289382	99.4458%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-502.noGEN.front	RAL-502.noGEN.front.gen	percent
uq reads:	2971859	730879	24.5933%
   reads: 	3289382	905046	27.5142%
----------------
match_TE:2:
  reads:	RAL-502.noGEN.front	RAL-502.noGEN.front.TE	percent
uq reads:	2971859	106374	3.5794%
   reads: 	3289382	109685	3.3345%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-502.noGEN.end	RAL-502.noGEN.end.gen	percent
uq reads:	2971859	573489	19.2973%
   reads: 	3289382	734583	22.3319%
----------------
match_TE:2:
  reads:	RAL-502.noGEN.end	RAL-502.noGEN.end.TE	percent
uq reads:	2971859	97041	3.2653%
   reads: 	3289382	101546	3.0871%
----------------
Candidate insertion sites in file: RAL-502_insert.txt
  reads:	13789
  uqreads:	13602
  Number of Candidate sites:	13602

Level 1 collapse of insertion sites in file: RAL-502_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	556

Level 1 annotation file: RAL-502_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-502_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-502.noGEN.front	RAL-502.noGEN.front.gendel	percent
uq reads:	2971859	743264	25.0101%
   reads: 	3289382	922480	28.0442%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-502.noGEN.end	RAL-502.noGEN.end.gendel	percent
uq reads:	2971859	583149	19.6224%
   reads: 	3289382	749486	22.7850%
----------------
Candidate breakpoint sites in file: RAL-502_depletion.xls
  reads:	35611
  uqreads:	34951
  Number of reads supporting candidate sites:	34951

Level 1 collapse of depletion sites in file: RAL-502_depletion_level1.xls
  Number of Level 1 collapsed sites:	3019