Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-306_75b.fastq.uq.polyn	RAL-306_75b.filter	percent
uq reads:	19610942	3120412	15.9116%
   reads: 	22121682	3510979	15.8712%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-306_75b.filter	RAL-306_75b.nostrna	percent
uq reads:	3120412	2305754	73.8926%
   reads: 	3510979	2519315	71.7553%
----------------
TE_filter:
  reads:	RAL-306_75b.nostrna	RAL-306_75b.noTE	percent
uq reads:	2305754	2299405	99.7246%
   reads: 	2519315	2511807	99.7020%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-306_75b.noGEN.front	RAL-306_75b.noGEN.front.gen	percent
uq reads:	2299405	938480	40.8140%
   reads: 	2511807	1026814	40.8795%
----------------
match_TE:2:
  reads:	RAL-306_75b.noGEN.front	RAL-306_75b.noGEN.front.TE	percent
uq reads:	2299405	128152	5.5733%
   reads: 	2511807	133572	5.3178%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-306_75b.noGEN.end	RAL-306_75b.noGEN.end.gen	percent
uq reads:	2299405	330692	14.3816%
   reads: 	2511807	416009	16.5621%
----------------
match_TE:2:
  reads:	RAL-306_75b.noGEN.end	RAL-306_75b.noGEN.end.TE	percent
uq reads:	2299405	62214	2.7057%
   reads: 	2511807	67647	2.6932%
----------------
Candidate insertion sites in file: RAL-306_75b_insert.txt
  reads:	5379
  uqreads:	4873
  Number of Candidate sites:	4873

Level 1 collapse of insertion sites in file: RAL-306_75b_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	312

Level 1 annotation file: RAL-306_75b_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-306_75b_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-306_75b.noGEN.front	RAL-306_75b.noGEN.front.gendel	percent
uq reads:	2299405	938480	40.8140%
   reads: 	2511807	1026814	40.8795%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-306_75b.noGEN.end	RAL-306_75b.noGEN.end.gendel	percent
uq reads:	2299405	330692	14.3816%
   reads: 	2511807	416009	16.5621%
----------------
Candidate breakpoint sites in file: RAL-306_75b_depletion.xls
  reads:	12157
  uqreads:	10512
  Number of reads supporting candidate sites:	10512

Level 1 collapse of depletion sites in file: RAL-306_75b_depletion_level1.xls
  Number of Level 1 collapsed sites:	1016