Table 1.

Genomic arithmetic used in the Coordinate Module to calculate chromosomal coordinates of embedded rNMPs

	rNMPs on forward strand		rNMPs on reverse strand
Technique	Start position	End position	Start position	End position
ribose-seq	end position (–) – 1	end position (–)	start position (+)	start position (+) + 1
HydEn-seq and Pu-seq	start position (+) – 1	start position (+)	end position (–)	end position (–) + 1
emRiboSeq	end position (–)	end position (–) + 1	start position (+) – 1	start position (+)

Chromosomal coordinates of embedded rNMPs are calculated based on the start/end positions of the reads (read 1) aligned to the reference genome. (+) = reads aligned to the forward strand of the reference genome and (–) = reads aligned to the reverse strand of the reference genome.