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Table 6 The quality of filled gaps reported by nanoGapFiller at different settings of pruning threshold MinimalMatchingProbability

From: Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph

Species Gap MinimalMatchingProbability
0 (%) \(10^{-8}\) (%) \(10^{-5}\) (default) (%) \(10^{-2}\) (%)
E. coli 252312r–252486r 87.22 87.22 87.22 87.22
E. coli 252486r–252526r 99.68 99.68 99.68 99.68
E. coli 252510r–252292r 98.87 98.87 98.87 96.55
E. coli 252196–252226 99.66 99.66 99.66 99.66
S. coelicolor 781738–781976r 100.00 100.00 100.00 100.00
S. coelicolor 781976r–781848r 100.00 100.00 100.00 100.00
P. putida 443944r–443818 99.88 99.88 99.88 99.88
  1. Here the gaps are identified using real optical maps and alignment method refAligner. The quality is measured using base-level similarity (NSS) between the filled gaps and the corresponding reference genome sequence