Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-177.fastq.uq.polyn	RAL-177.filter	percent
uq reads:	41648961	3806834	9.1403%
   reads: 	48196755	5487234	11.3851%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-177.filter	RAL-177.nostrna	percent
uq reads:	3806834	3706970	97.3767%
   reads: 	5487234	5045770	91.9547%
----------------
TE_filter:
  reads:	RAL-177.nostrna	RAL-177.noTE	percent
uq reads:	3706970	3695760	99.6976%
   reads: 	5045770	5029998	99.6874%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-177.noGEN.front	RAL-177.noGEN.front.gen	percent
uq reads:	3695760	1168741	31.6238%
   reads: 	5029998	1409771	28.0273%
----------------
match_TE:2:
  reads:	RAL-177.noGEN.front	RAL-177.noGEN.front.TE	percent
uq reads:	3695760	195291	5.2842%
   reads: 	5029998	214558	4.2656%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-177.noGEN.end	RAL-177.noGEN.end.gen	percent
uq reads:	3695760	1117636	30.2410%
   reads: 	5029998	1362869	27.0948%
----------------
match_TE:2:
  reads:	RAL-177.noGEN.end	RAL-177.noGEN.end.TE	percent
uq reads:	3695760	194371	5.2593%
   reads: 	5029998	214665	4.2677%
----------------
Candidate insertion sites in file: RAL-177_insert.txt
  reads:	39429
  uqreads:	38248
  Number of Candidate sites:	38248

Level 1 collapse of insertion sites in file: RAL-177_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	627

Level 1 annotation file: RAL-177_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-177_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-177.noGEN.front	RAL-177.noGEN.front.gendel	percent
uq reads:	3695760	1192450	32.2654%
   reads: 	5029998	1436134	28.5514%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-177.noGEN.end	RAL-177.noGEN.end.gendel	percent
uq reads:	3695760	1138931	30.8172%
   reads: 	5029998	1386594	27.5665%
----------------
Candidate breakpoint sites in file: RAL-177_depletion.xls
  reads:	76668
  uqreads:	73526
  Number of reads supporting candidate sites:	73526

Level 1 collapse of depletion sites in file: RAL-177_depletion_level1.xls
  Number of Level 1 collapsed sites:	3076