Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-26.fastq.uq.polyn	RAL-26.filter	percent
uq reads:	29340438	1408129	4.7993%
   reads: 	31886511	1711002	5.3659%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-26.filter	RAL-26.nostrna	percent
uq reads:	1408129	1377242	97.8065%
   reads: 	1711002	1672615	97.7565%
----------------
TE_filter:
  reads:	RAL-26.nostrna	RAL-26.noTE	percent
uq reads:	1377242	1370409	99.5039%
   reads: 	1672615	1662708	99.4077%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-26.noGEN.front	RAL-26.noGEN.front.gen	percent
uq reads:	1370409	518520	37.8369%
   reads: 	1662708	713209	42.8944%
----------------
match_TE:2:
  reads:	RAL-26.noGEN.front	RAL-26.noGEN.front.TE	percent
uq reads:	1370409	71318	5.2041%
   reads: 	1662708	74366	4.4726%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-26.noGEN.end	RAL-26.noGEN.end.gen	percent
uq reads:	1370409	365244	26.6522%
   reads: 	1662708	549068	33.0225%
----------------
match_TE:2:
  reads:	RAL-26.noGEN.end	RAL-26.noGEN.end.TE	percent
uq reads:	1370409	62416	4.5546%
   reads: 	1662708	65837	3.9596%
----------------
Candidate insertion sites in file: RAL-26_insert.txt
  reads:	6712
  uqreads:	6470
  Number of Candidate sites:	6470

Level 1 collapse of insertion sites in file: RAL-26_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	396

Level 1 annotation file: RAL-26_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-26_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-26.noGEN.front	RAL-26.noGEN.front.gendel	percent
uq reads:	1370409	518520	37.8369%
   reads: 	1662708	713209	42.8944%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-26.noGEN.end	RAL-26.noGEN.end.gendel	percent
uq reads:	1370409	365244	26.6522%
   reads: 	1662708	549068	33.0225%
----------------
Candidate breakpoint sites in file: RAL-26_depletion.xls
  reads:	16898
  uqreads:	16102
  Number of reads supporting candidate sites:	16102

Level 1 collapse of depletion sites in file: RAL-26_depletion_level1.xls
  Number of Level 1 collapsed sites:	1551