Table 1 Description of alignment attributes. Each attribute is contained within a separate metadata column in the GRanges object

seqnames

Chromosome on which the aligned read is mapped.

ranges

Start and end position of the alignment in genomic coordinates.

strand

Strand to which the aligned read is mapped.

sample

Sample name from which the alignment originates.

exp

Experiment type of the sample from which the alignment originates, either ‘Ribo’ for Ribo-seq, or ‘RNA’ for RNA-seq.

length

Length of the aligned read in nucleotides.

gene

Gene to which the read is mapped. Corresponds to Gene IDs within the provided annotation file. ‘Other’ if not mapped within a gene.

feature

Feature type to which the read is mapped. Feature types correspond to those included in the user-provided annotation file.

pos

Genomic position of alignment based on p-site adjustment.

start_dist

Distance from transcription start site (TSS) of a gene to p-site position, in transcript coordinates (with introns removed). The major isoform of each gene is used to calculate this distance.

end_dist

Distance from p-site position to translation stop codon (TSC) of a gene, in transcript coordinates (with introns removed). The major isoform of each gene is used to calculate this distance.

gc

The percentage of nucleotides in the aligned read which are G’s or C’s.

mapq

The mapq score of the alignment. Typically, alignments with a mapq score of 50 are considered uniquely mapped, while all other scores are considered multi-mapping.

frame

The trinucleotide frame of a read’s p-site, relative to the TSS of the gene’s major isoform. Reads that map within an mRNA are assigned either a 0, 1, or 2, while reads which map outside the mRNA are assigned ‘none’.