Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-391_95b.fastq.uq.polyn	RAL-391_95b.filter	percent
uq reads:	33290575	1954224	5.8702%
   reads: 	37297862	2569381	6.8888%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-391_95b.filter	RAL-391_95b.nostrna	percent
uq reads:	1954224	1900963	97.2746%
   reads: 	2569381	2378638	92.5763%
----------------
TE_filter:
  reads:	RAL-391_95b.nostrna	RAL-391_95b.noTE	percent
uq reads:	1900963	1896061	99.7421%
   reads: 	2378638	2371864	99.7152%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-391_95b.noGEN.front	RAL-391_95b.noGEN.front.gen	percent
uq reads:	1896061	616110	32.4942%
   reads: 	2371864	751360	31.6780%
----------------
match_TE:2:
  reads:	RAL-391_95b.noGEN.front	RAL-391_95b.noGEN.front.TE	percent
uq reads:	1896061	97185	5.1256%
   reads: 	2371864	106833	4.5042%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-391_95b.noGEN.end	RAL-391_95b.noGEN.end.gen	percent
uq reads:	1896061	403869	21.3004%
   reads: 	2371864	530290	22.3575%
----------------
match_TE:2:
  reads:	RAL-391_95b.noGEN.end	RAL-391_95b.noGEN.end.TE	percent
uq reads:	1896061	79724	4.2047%
   reads: 	2371864	90185	3.8023%
----------------
Candidate insertion sites in file: RAL-391_95b_insert.txt
  reads:	14469
  uqreads:	13928
  Number of Candidate sites:	13928

Level 1 collapse of insertion sites in file: RAL-391_95b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	641

Level 1 annotation file: RAL-391_95b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-391_95b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-391_95b.noGEN.front	RAL-391_95b.noGEN.front.gendel	percent
uq reads:	1896061	616110	32.4942%
   reads: 	2371864	751360	31.6780%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-391_95b.noGEN.end	RAL-391_95b.noGEN.end.gendel	percent
uq reads:	1896061	403869	21.3004%
   reads: 	2371864	530290	22.3575%
----------------
Candidate breakpoint sites in file: RAL-391_95b_depletion.xls
  reads:	35259
  uqreads:	33793
  Number of reads supporting candidate sites:	33793

Level 1 collapse of depletion sites in file: RAL-391_95b_depletion_level1.xls
  Number of Level 1 collapsed sites:	3049