Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-832.fastq.uq.polyn	RAL-832.filter	percent
uq reads:	31126620	4824530	15.4997%
   reads: 	32801178	5377171	16.3932%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-832.filter	RAL-832.nostrna	percent
uq reads:	4824530	2081572	43.1456%
   reads: 	5377171	2336826	43.4583%
----------------
TE_filter:
  reads:	RAL-832.nostrna	RAL-832.noTE	percent
uq reads:	2081572	2070572	99.4716%
   reads: 	2336826	2325440	99.5128%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-832.noGEN.front	RAL-832.noGEN.front.gen	percent
uq reads:	2070572	594478	28.7108%
   reads: 	2325440	662201	28.4764%
----------------
match_TE:2:
  reads:	RAL-832.noGEN.front	RAL-832.noGEN.front.TE	percent
uq reads:	2070572	82971	4.0072%
   reads: 	2325440	89591	3.8526%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-832.noGEN.end	RAL-832.noGEN.end.gen	percent
uq reads:	2070572	493906	23.8536%
   reads: 	2325440	557861	23.9895%
----------------
match_TE:2:
  reads:	RAL-832.noGEN.end	RAL-832.noGEN.end.TE	percent
uq reads:	2070572	78297	3.7814%
   reads: 	2325440	85810	3.6901%
----------------
Candidate insertion sites in file: RAL-832_insert.txt
  reads:	10358
  uqreads:	10229
  Number of Candidate sites:	10229

Level 1 collapse of insertion sites in file: RAL-832_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	498

Level 1 annotation file: RAL-832_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-832_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-832.noGEN.front	RAL-832.noGEN.front.gendel	percent
uq reads:	2070572	603778	29.1600%
   reads: 	2325440	672445	28.9169%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-832.noGEN.end	RAL-832.noGEN.end.gendel	percent
uq reads:	2070572	502003	24.2447%
   reads: 	2325440	566837	24.3755%
----------------
Candidate breakpoint sites in file: RAL-832_depletion.xls
  reads:	23867
  uqreads:	23521
  Number of reads supporting candidate sites:	23521

Level 1 collapse of depletion sites in file: RAL-832_depletion_level1.xls
  Number of Level 1 collapsed sites:	2039