For microbial organisms, reads were aligned to the complete reference sequences, but only chromosomal contigs were considered in the bias calculations. For human data, reads were aligned to the complete reference sequence, but only autosomal contigs were considered in bias calculations. Plasmid, mitochondrial, and sex chromosomes were not included because they are not expected to be equimolar with the rest of the genome. Regions of the references containing ambiguous bases were also excluded from all bias computations as there is no way to accurately map reads to them or to assess their membership in motifs.
