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Table 1 A summary of simulation data and real data used in the analysis

From: NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data

Datasets #base in ref a #reads b #modification c Modification types
100 ‘MeanDif’ simulation datasets 6184-bp 200 in each dataset a group of 60 modifications Only signal mean of modified bases was affected without neighborhood effect.
100 ‘STDDif’ simulation datasets 6184-bp 200 in each dataset a group of 60 modifications Only signal standard deviation of modified bases was affected without neighborhood effect.
100 ‘Mean_STDDif’ simulation datasets 6184-bp 200 in each dataset a group of 60 modifications Both signal mean and standard deviation of modified bases were affected without neighborhood effect.
100 ‘Mean_STDDif_NE’ simulation datasets 6184-bp 200 in each dataset a group of 60 modifications Both signal mean and standard deviation of modified bases were affected with neighborhood effect.
E. coli [3] ~ 4.64 Mb 181,092 693,586 Methylation at all CpG sites
  1. aThe number of bases in the reference sequence
  2. bThe number of reads in a dataset. For simulation data, half of reads have modifications and the other half do not have modifications. For E. Coli, 111,213 reads have methylations and 69,879 do not have methylations
  3. cThe number of modifications in each dataset