Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-385.fastq.uq.polyn	RAL-385.filter	percent
uq reads:	21684409	3093305	14.2651%
   reads: 	23706924	3590426	15.1451%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-385.filter	RAL-385.nostrna	percent
uq reads:	3093305	2976284	96.2170%
   reads: 	3590426	3453829	96.1955%
----------------
TE_filter:
  reads:	RAL-385.nostrna	RAL-385.noTE	percent
uq reads:	2976284	2969333	99.7665%
   reads: 	3453829	3446618	99.7912%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-385.noGEN.front	RAL-385.noGEN.front.gen	percent
uq reads:	2969333	684294	23.0454%
   reads: 	3446618	786656	22.8240%
----------------
match_TE:2:
  reads:	RAL-385.noGEN.front	RAL-385.noGEN.front.TE	percent
uq reads:	2969333	91549	3.0832%
   reads: 	3446618	102207	2.9654%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-385.noGEN.end	RAL-385.noGEN.end.gen	percent
uq reads:	2969333	554584	18.6771%
   reads: 	3446618	646658	18.7621%
----------------
match_TE:2:
  reads:	RAL-385.noGEN.end	RAL-385.noGEN.end.TE	percent
uq reads:	2969333	87486	2.9463%
   reads: 	3446618	100488	2.9156%
----------------
Candidate insertion sites in file: RAL-385_insert.txt
  reads:	8129
  uqreads:	7985
  Number of Candidate sites:	7985

Level 1 collapse of insertion sites in file: RAL-385_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	384

Level 1 annotation file: RAL-385_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-385_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-385.noGEN.front	RAL-385.noGEN.front.gendel	percent
uq reads:	2969333	694413	23.3862%
   reads: 	3446618	797753	23.1460%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-385.noGEN.end	RAL-385.noGEN.end.gendel	percent
uq reads:	2969333	563549	18.9790%
   reads: 	3446618	657063	19.0640%
----------------
Candidate breakpoint sites in file: RAL-385_depletion.xls
  reads:	16799
  uqreads:	16596
  Number of reads supporting candidate sites:	16596

Level 1 collapse of depletion sites in file: RAL-385_depletion_level1.xls
  Number of Level 1 collapsed sites:	1322