Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-88.fastq.uq.polyn	RAL-88.filter	percent
uq reads:	30070734	1661927	5.5267%
   reads: 	31639454	1935923	6.1187%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-88.filter	RAL-88.nostrna	percent
uq reads:	1661927	1617555	97.3301%
   reads: 	1935923	1886290	97.4362%
----------------
TE_filter:
  reads:	RAL-88.nostrna	RAL-88.noTE	percent
uq reads:	1617555	1609820	99.5218%
   reads: 	1886290	1877570	99.5377%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-88.noGEN.front	RAL-88.noGEN.front.gen	percent
uq reads:	1609820	654072	40.6301%
   reads: 	1877570	810942	43.1910%
----------------
match_TE:2:
  reads:	RAL-88.noGEN.front	RAL-88.noGEN.front.TE	percent
uq reads:	1609820	91272	5.6697%
   reads: 	1877570	94628	5.0399%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-88.noGEN.end	RAL-88.noGEN.end.gen	percent
uq reads:	1609820	560050	34.7896%
   reads: 	1877570	709210	37.7728%
----------------
match_TE:2:
  reads:	RAL-88.noGEN.end	RAL-88.noGEN.end.TE	percent
uq reads:	1609820	87141	5.4131%
   reads: 	1877570	90947	4.8439%
----------------
Candidate insertion sites in file: RAL-88_insert.txt
  reads:	8084
  uqreads:	7971
  Number of Candidate sites:	7971

Level 1 collapse of insertion sites in file: RAL-88_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	506

Level 1 annotation file: RAL-88_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-88_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-88.noGEN.front	RAL-88.noGEN.front.gendel	percent
uq reads:	1609820	654072	40.6301%
   reads: 	1877570	810942	43.1910%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-88.noGEN.end	RAL-88.noGEN.end.gendel	percent
uq reads:	1609820	560050	34.7896%
   reads: 	1877570	709210	37.7728%
----------------
Candidate breakpoint sites in file: RAL-88_depletion.xls
  reads:	17329
  uqreads:	16950
  Number of reads supporting candidate sites:	16950

Level 1 collapse of depletion sites in file: RAL-88_depletion_level1.xls
  Number of Level 1 collapsed sites:	1637