Insertion Pipeline
Bowtie2_wholegenome:
  reads:	RAL-819.fastq.uq.polyn	RAL-819.filter	percent
uq reads:	129402156	17459262	13.4922%
   reads: 	149204440	20949146	14.0406%
----------------
virus_structural_rna_repbase_filter:
  reads:	RAL-819.filter	RAL-819.nostrna	percent
uq reads:	17459262	15721294	90.0456%
   reads: 	20949146	18543070	88.5147%
----------------
TE_filter:
  reads:	RAL-819.nostrna	RAL-819.noTE	percent
uq reads:	15721294	15693530	99.8234%
   reads: 	18543070	18500558	99.7707%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-819.noGEN.front	RAL-819.noGEN.front.gen	percent
uq reads:	15693530	2588984	16.4971%
   reads: 	18500558	3414796	18.4578%
----------------
match_TE:2:
  reads:	RAL-819.noGEN.front	RAL-819.noGEN.front.TE	percent
uq reads:	15693530	407535	2.5968%
   reads: 	18500558	459101	2.4816%
----------------
match_dm6_mask_gen:1:
  reads:	RAL-819.noGEN.end	RAL-819.noGEN.end.gen	percent
uq reads:	15693530	1390292	8.8590%
   reads: 	18500558	2212941	11.9615%
----------------
match_TE:2:
  reads:	RAL-819.noGEN.end	RAL-819.noGEN.end.TE	percent
uq reads:	15693530	279583	1.7815%
   reads: 	18500558	329469	1.7809%
----------------
Candidate insertion sites in file: RAL-819_insert.txt
  reads:	50092
  uqreads:	45558
  Number of Candidate sites:	45558

Level 1 collapse of insertion sites in file: RAL-819_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	751

Level 1 annotation file: RAL-819_level1siteannotation.xls
Insertion sites in fixed bin:
RAL-819_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	RAL-819.noGEN.front	RAL-819.noGEN.front.gendel	percent
uq reads:	15693530	2588984	16.4971%
   reads: 	18500558	3414796	18.4578%
----------------
match_dm6_mask_gen_del:1:
  reads:	RAL-819.noGEN.end	RAL-819.noGEN.end.gendel	percent
uq reads:	15693530	1390292	8.8590%
   reads: 	18500558	2212941	11.9615%
----------------
Candidate breakpoint sites in file: RAL-819_depletion.xls
  reads:	126873
  uqreads:	113131
  Number of reads supporting candidate sites:	113131

Level 1 collapse of depletion sites in file: RAL-819_depletion_level1.xls
  Number of Level 1 collapsed sites:	4355