Table 1 Nanopore sequencing data sets used to evaluate DeepMod

From: Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

Genome Data set name Motif # reads Coverage Metha Reference
Escherichia coli UMR NAd 111,238 110X Negb Simpson et al. 4
CG_MsssI CGc 69,899 67X 5mC  
CG_SssI CGc 8679 19X 5mC  
CG_MpeI CGc 23,593 39X 5mC  
GCGC_HhaI GCGCc 18,180 50X 5mC  
gaAttc_EcoRI GAATTCc 16,661 27X 6mA Stoiber et al. 3
gAtc_dam GATCc 17,557 33X 6mA  
tcgA_TaqI TCGAc 16,249 22X 6mA  
Con1 NAd 23,762 34X Negb  
Con2 NAd 34,170 40X Negb  
Homo sapiens NA12878 CGc   30X 5mC Jain et al. 31
HX1 CGc 4,827,155 30X 5mC Current study
Chlamydomonas reinhardtii C. reinhardtii NAd 772,817 126X 6mA Current study
  1. a Methylation types
  2. b Negative control without any modifications
  3. c Underlined nucleotides in motifs were potential modified target.
  4. d No modifications or no motif information