Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-315_75b.fastq.uq.polyn	RAL-315_75b.filter	percent
uq reads:	17677163	2130940	12.0548%
   reads: 	20021592	2361800	11.7963%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-315_75b.filter	RAL-315_75b.nostrna	percent
uq reads:	2130940	2098737	98.4888%
   reads: 	2361800	2309472	97.7844%
----------------
TE_filter:
  reads:	RAL-315_75b.nostrna	RAL-315_75b.noTE	percent
uq reads:	2098737	2094848	99.8147%
   reads: 	2309472	2304814	99.7983%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-315_75b.noGEN.front	RAL-315_75b.noGEN.front.gen	percent
uq reads:	2094848	1055211	50.3717%
   reads: 	2304814	1140462	49.4817%
----------------
match_TE:2:
  reads:	RAL-315_75b.noGEN.front	RAL-315_75b.noGEN.front.TE	percent
uq reads:	2094848	124959	5.9651%
   reads: 	2304814	130498	5.6620%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-315_75b.noGEN.end	RAL-315_75b.noGEN.end.gen	percent
uq reads:	2094848	259033	12.3652%
   reads: 	2304814	334294	14.5042%
----------------
match_TE:2:
  reads:	RAL-315_75b.noGEN.end	RAL-315_75b.noGEN.end.TE	percent
uq reads:	2094848	43786	2.0902%
   reads: 	2304814	48562	2.1070%
----------------
Candidate insertion sites in file: RAL-315_75b_insert.txt
  reads:	4513
  uqreads:	4110
  Number of Candidate sites:	4110

Level 1 collapse of insertion sites in file: RAL-315_75b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	286

Level 1 annotation file: RAL-315_75b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-315_75b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-315_75b.noGEN.front	RAL-315_75b.noGEN.front.gendel	percent
uq reads:	2094848	1055211	50.3717%
   reads: 	2304814	1140462	49.4817%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-315_75b.noGEN.end	RAL-315_75b.noGEN.end.gendel	percent
uq reads:	2094848	259033	12.3652%
   reads: 	2304814	334294	14.5042%
----------------
Candidate breakpoint sites in file: RAL-315_75b_depletion.xls
  reads:	10605
  uqreads:	9237
  Number of reads supporting candidate sites:	9237

Level 1 collapse of depletion sites in file: RAL-315_75b_depletion_level1.xls
  Number of Level 1 collapsed sites:	825