Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-379.fastq.uq.polyn	RAL-379.filter	percent
uq reads:	17456090	2061899	11.8119%
   reads: 	18289824	2237553	12.2339%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-379.filter	RAL-379.nostrna	percent
uq reads:	2061899	2034053	98.6495%
   reads: 	2237553	2198311	98.2462%
----------------
TE_filter:
  reads:	RAL-379.nostrna	RAL-379.noTE	percent
uq reads:	2034053	2027282	99.6671%
   reads: 	2198311	2190817	99.6591%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-379.noGEN.front	RAL-379.noGEN.front.gen	percent
uq reads:	2027282	768293	37.8977%
   reads: 	2190817	848126	38.7128%
----------------
match_TE:2:
  reads:	RAL-379.noGEN.front	RAL-379.noGEN.front.TE	percent
uq reads:	2027282	100347	4.9498%
   reads: 	2190817	103029	4.7028%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-379.noGEN.end	RAL-379.noGEN.end.gen	percent
uq reads:	2027282	228030	11.2481%
   reads: 	2190817	306823	14.0050%
----------------
match_TE:2:
  reads:	RAL-379.noGEN.end	RAL-379.noGEN.end.TE	percent
uq reads:	2027282	46392	2.2884%
   reads: 	2190817	49373	2.2536%
----------------
Candidate insertion sites in file: RAL-379_insert.txt
  reads:	3862
  uqreads:	3823
  Number of Candidate sites:	3823

Level 1 collapse of insertion sites in file: RAL-379_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	268

Level 1 annotation file: RAL-379_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-379_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-379.noGEN.front	RAL-379.noGEN.front.gendel	percent
uq reads:	2027282	768293	37.8977%
   reads: 	2190817	848126	38.7128%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-379.noGEN.end	RAL-379.noGEN.end.gendel	percent
uq reads:	2027282	228030	11.2481%
   reads: 	2190817	306823	14.0050%
----------------
Candidate breakpoint sites in file: RAL-379_depletion.xls
  reads:	9173
  uqreads:	8894
  Number of reads supporting candidate sites:	8894

Level 1 collapse of depletion sites in file: RAL-379_depletion_level1.xls
  Number of Level 1 collapsed sites:	777