Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-129.fastq.uq.polyn	RAL-129.filter	percent
uq reads:	24767102	1653571	6.6765%
   reads: 	26578217	2008139	7.5556%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-129.filter	RAL-129.nostrna	percent
uq reads:	1653571	1579303	95.5086%
   reads: 	2008139	1903917	94.8100%
----------------
TE_filter:
  reads:	RAL-129.nostrna	RAL-129.noTE	percent
uq reads:	1579303	1563350	98.9899%
   reads: 	1903917	1886021	99.0600%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-129.noGEN.front	RAL-129.noGEN.front.gen	percent
uq reads:	1563350	475740	30.4308%
   reads: 	1886021	657170	34.8443%
----------------
match_TE:2:
  reads:	RAL-129.noGEN.front	RAL-129.noGEN.front.TE	percent
uq reads:	1563350	79837	5.1068%
   reads: 	1886021	86120	4.5662%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-129.noGEN.end	RAL-129.noGEN.end.gen	percent
uq reads:	1563350	397542	25.4289%
   reads: 	1886021	569260	30.1831%
----------------
match_TE:2:
  reads:	RAL-129.noGEN.end	RAL-129.noGEN.end.TE	percent
uq reads:	1563350	73660	4.7117%
   reads: 	1886021	80500	4.2682%
----------------
Candidate insertion sites in file: RAL-129_insert.txt
  reads:	6650
  uqreads:	6547
  Number of Candidate sites:	6547

Level 1 collapse of insertion sites in file: RAL-129_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	429

Level 1 annotation file: RAL-129_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-129_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-129.noGEN.front	RAL-129.noGEN.front.gendel	percent
uq reads:	1563350	475740	30.4308%
   reads: 	1886021	657170	34.8443%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-129.noGEN.end	RAL-129.noGEN.end.gendel	percent
uq reads:	1563350	397542	25.4289%
   reads: 	1886021	569260	30.1831%
----------------
Candidate breakpoint sites in file: RAL-129_depletion.xls
  reads:	13119
  uqreads:	12778
  Number of reads supporting candidate sites:	12778

Level 1 collapse of depletion sites in file: RAL-129_depletion_level1.xls
  Number of Level 1 collapsed sites:	1181