a, The retrieved viromes were mapped against rRNA small and large subunits reference sequences (x axis) and against 31 single-copy bacterial markers (y axis). The scatter plot shows the percentage of aligned reads on 1,751 human and animal viromes (purple) and 226 environmental viromes (blue). The dotted lines indicate the median abundances in the corresponding metagenomes. b, Spearman’s correlation coefficients between the 31 single-copy markers and the small and large subunits of the rRNA gene. c, Fraction of the discarded viromes at different enrichment thresholds (dashed lines) and using different components to calculate the enrichment. The proposed score (rRNA SSU + LSU + single-copy markers) is drawn in black. d, Enrichment scores of samples within each dataset grouped by dataset type, together with metagenomes used as controls. The enrichment score is based on both SSU and LSU rRNAs and single-copy markers. References to each dataset are provided in Supplementary Tables 1 and 2.