Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-229_125b.fastq.uq.polyn	RAL-229_125b.filter	percent
uq reads:	63014882	8769505	13.9166%
   reads: 	70518505	9957600	14.1205%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-229_125b.filter	RAL-229_125b.nostrna	percent
uq reads:	8769505	8722646	99.4657%
   reads: 	9957600	9854165	98.9612%
----------------
TE_filter:
  reads:	RAL-229_125b.nostrna	RAL-229_125b.noTE	percent
uq reads:	8722646	8710074	99.8559%
   reads: 	9854165	9836430	99.8200%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-229_125b.noGEN.front	RAL-229_125b.noGEN.front.gen	percent
uq reads:	8710074	2283421	26.2159%
   reads: 	9836430	2585990	26.2899%
----------------
match_TE:2:
  reads:	RAL-229_125b.noGEN.front	RAL-229_125b.noGEN.front.TE	percent
uq reads:	8710074	353261	4.0558%
   reads: 	9836430	367929	3.7405%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-229_125b.noGEN.end	RAL-229_125b.noGEN.end.gen	percent
uq reads:	8710074	637956	7.3243%
   reads: 	9836430	932871	9.4838%
----------------
match_TE:2:
  reads:	RAL-229_125b.noGEN.end	RAL-229_125b.noGEN.end.TE	percent
uq reads:	8710074	142777	1.6392%
   reads: 	9836430	156884	1.5949%
----------------
Candidate insertion sites in file: RAL-229_125b_insert.txt
  reads:	30160
  uqreads:	28362
  Number of Candidate sites:	28362

Level 1 collapse of insertion sites in file: RAL-229_125b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	642

Level 1 annotation file: RAL-229_125b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-229_125b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-229_125b.noGEN.front	RAL-229_125b.noGEN.front.gendel	percent
uq reads:	8710074	2283421	26.2159%
   reads: 	9836430	2585990	26.2899%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-229_125b.noGEN.end	RAL-229_125b.noGEN.end.gendel	percent
uq reads:	8710074	637956	7.3243%
   reads: 	9836430	932871	9.4838%
----------------
Candidate breakpoint sites in file: RAL-229_125b_depletion.xls
  reads:	86707
  uqreads:	80405
  Number of reads supporting candidate sites:	80405

Level 1 collapse of depletion sites in file: RAL-229_125b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3946