Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-332.fastq.uq.polyn	RAL-332.filter	percent
uq reads:	61935436	3702565	5.9781%
   reads: 	65057945	4285296	6.5869%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-332.filter	RAL-332.nostrna	percent
uq reads:	3702565	3593859	97.0640%
   reads: 	4285296	4162597	97.1367%
----------------
TE_filter:
  reads:	RAL-332.nostrna	RAL-332.noTE	percent
uq reads:	3593859	3557857	98.9982%
   reads: 	4162597	4122636	99.0400%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-332.noGEN.front	RAL-332.noGEN.front.gen	percent
uq reads:	3557857	1076653	30.2613%
   reads: 	4122636	1413158	34.2780%
----------------
match_TE:2:
  reads:	RAL-332.noGEN.front	RAL-332.noGEN.front.TE	percent
uq reads:	3557857	144765	4.0689%
   reads: 	4122636	151107	3.6653%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-332.noGEN.end	RAL-332.noGEN.end.gen	percent
uq reads:	3557857	892339	25.0808%
   reads: 	4122636	1212161	29.4026%
----------------
match_TE:2:
  reads:	RAL-332.noGEN.end	RAL-332.noGEN.end.TE	percent
uq reads:	3557857	133460	3.7511%
   reads: 	4122636	141259	3.4264%
----------------
Candidate insertion sites in file: RAL-332_insert.txt
  reads:	11559
  uqreads:	11386
  Number of Candidate sites:	11386

Level 1 collapse of insertion sites in file: RAL-332_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	575

Level 1 annotation file: RAL-332_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-332_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-332.noGEN.front	RAL-332.noGEN.front.gendel	percent
uq reads:	3557857	1076653	30.2613%
   reads: 	4122636	1413158	34.2780%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-332.noGEN.end	RAL-332.noGEN.end.gendel	percent
uq reads:	3557857	892339	25.0808%
   reads: 	4122636	1212161	29.4026%
----------------
Candidate breakpoint sites in file: RAL-332_depletion.xls
  reads:	27158
  uqreads:	26342
  Number of reads supporting candidate sites:	26342

Level 1 collapse of depletion sites in file: RAL-332_depletion_level1.xls
  Number of Level 1 collapsed sites:	2202