Presence of reference minor alleles (RMA) (A) and low-mappability regions (B) in the major human reference genome assemblies used for human genetic variation analysis—b37, hg38 (with either all or only primary contigs), and the new T2T assembly [89]. On (A), RMA sites in T2T are separated according to their concordance with hg38. On (B), the number of bases with a fraction of non-uniquely mapped reads > 0.4 (left) or 0.95 (right) is shown for the gold-standard GIAB WES datasets (HG001–HG007) used in our recent study [15].