Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-810.fastq.uq.polyn	RAL-810.filter	percent
uq reads:	30471776	1668027	5.4740%
   reads: 	36469808	2977817	8.1652%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-810.filter	RAL-810.nostrna	percent
uq reads:	1668027	1557488	93.3731%
   reads: 	2977817	2467681	82.8688%
----------------
TE_filter:
  reads:	RAL-810.nostrna	RAL-810.noTE	percent
uq reads:	1557488	1547385	99.3513%
   reads: 	2467681	2450457	99.3020%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-810.noGEN.front	RAL-810.noGEN.front.gen	percent
uq reads:	1547385	506222	32.7147%
   reads: 	2450457	803745	32.7998%
----------------
match_TE:2:
  reads:	RAL-810.noGEN.front	RAL-810.noGEN.front.TE	percent
uq reads:	1547385	74094	4.7883%
   reads: 	2450457	102260	4.1731%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-810.noGEN.end	RAL-810.noGEN.end.gen	percent
uq reads:	1547385	461789	29.8432%
   reads: 	2450457	754241	30.7796%
----------------
match_TE:2:
  reads:	RAL-810.noGEN.end	RAL-810.noGEN.end.TE	percent
uq reads:	1547385	73913	4.7766%
   reads: 	2450457	105854	4.3198%
----------------
Candidate insertion sites in file: RAL-810_insert.txt
  reads:	11451
  uqreads:	10658
  Number of Candidate sites:	10658

Level 1 collapse of insertion sites in file: RAL-810_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	555

Level 1 annotation file: RAL-810_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-810_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-810.noGEN.front	RAL-810.noGEN.front.gendel	percent
uq reads:	1547385	506222	32.7147%
   reads: 	2450457	803745	32.7998%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-810.noGEN.end	RAL-810.noGEN.end.gendel	percent
uq reads:	1547385	461789	29.8432%
   reads: 	2450457	754241	30.7796%
----------------
Candidate breakpoint sites in file: RAL-810_depletion.xls
  reads:	23478
  uqreads:	21895
  Number of reads supporting candidate sites:	21895

Level 1 collapse of depletion sites in file: RAL-810_depletion_level1.xls
  Number of Level 1 collapsed sites:	2279