Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-439.fastq.uq.polyn	RAL-439.filter	percent
uq reads:	33470216	2585953	7.7261%
   reads: 	36786629	3256927	8.8536%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-439.filter	RAL-439.nostrna	percent
uq reads:	2585953	2359104	91.2276%
   reads: 	3256927	2860819	87.8380%
----------------
TE_filter:
  reads:	RAL-439.nostrna	RAL-439.noTE	percent
uq reads:	2359104	2345286	99.4143%
   reads: 	2860819	2845895	99.4783%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-439.noGEN.front	RAL-439.noGEN.front.gen	percent
uq reads:	2345286	529643	22.5833%
   reads: 	2845895	621414	21.8355%
----------------
match_TE:2:
  reads:	RAL-439.noGEN.front	RAL-439.noGEN.front.TE	percent
uq reads:	2345286	66190	2.8223%
   reads: 	2845895	77852	2.7356%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-439.noGEN.end	RAL-439.noGEN.end.gen	percent
uq reads:	2345286	621275	26.4904%
   reads: 	2845895	713738	25.0796%
----------------
match_TE:2:
  reads:	RAL-439.noGEN.end	RAL-439.noGEN.end.TE	percent
uq reads:	2345286	79582	3.3933%
   reads: 	2845895	92841	3.2623%
----------------
Candidate insertion sites in file: RAL-439_insert.txt
  reads:	10137
  uqreads:	9939
  Number of Candidate sites:	9939

Level 1 collapse of insertion sites in file: RAL-439_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	511

Level 1 annotation file: RAL-439_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-439_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-439.noGEN.front	RAL-439.noGEN.front.gendel	percent
uq reads:	2345286	537033	22.8984%
   reads: 	2845895	631308	22.1831%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-439.noGEN.end	RAL-439.noGEN.end.gendel	percent
uq reads:	2345286	630348	26.8772%
   reads: 	2845895	724512	25.4581%
----------------
Candidate breakpoint sites in file: RAL-439_depletion.xls
  reads:	26372
  uqreads:	25774
  Number of reads supporting candidate sites:	25774

Level 1 collapse of depletion sites in file: RAL-439_depletion_level1.xls
  Number of Level 1 collapsed sites:	2275