We find that a typical genome differs from the reference human genome at 4.1 million to 5.0 million sites (Fig. 1b and Table 1). Although >99.9% of variants consist of SNPs and short indels, structural variants affect more bases: the typical genome contains an estimated 2,100 to 2,500 structural variants (∼1,000 large deletions, ∼160 copy-number variants, ∼915 Alu insertions, ∼128 L1 insertions, ∼51 SVA insertions, ∼4 NUMTs, and ∼10 inversions), affecting ∼20 million bases of sequence.Table 1Median autosomal variant sites per genomeAFRAMREASEURSASSamples661347504503489Mean coverage8.27.67.77.48.0Var. sitesSingletonsVar. sitesSingletonsVar. sitesSingletonsVar. sitesSingletonsVar. sitesSingletonsSNPs4.31M14.5k3.64M12.0k3.55M14.8k3.53M11.4k3.60M14.4kIndels625k-557k-546k-546k-556k-Large deletions1.1k59495940793959475CNVs17011531158115711651MEI (Alu)1.03k08450899191908890MEI (L1)13801180130012301230MEI (SVA)520440560530440MEI (MT)5050404040Inversions1209010090110Nonsynon12.2k13910.4k12110.2k14410.2k11610.3k144Synon13.8k7811.4k6711.2k7911.2k5911.4k78Intron2.06M7.33k1.72M6.12k1.68M7.39k1.68M5.68k1.72M7.20kUTR37.2k16830.8k13630.0k16930.0k12930.7k168Promoter102k43084.3k33281.6k42582.2k33684.0k430Insulator70.9k24859.0k19957.7k25257.7k18959.1k243Enhancer354k1.32k295k1.05k289k1.34k288k1.02k295k1.31kTFBSs92747593748474937653Filtered LoF18241523153414931513HGMD-DM200180161182160GWAS2.00k02.07k01.99k02.08k02.06k0ClinVar280301240291271See Supplementary Table 1 for continental population groupings. CNVs, copy-number variants; HGMD-DM, Human Gene Mutation Database disease mutations; k, thousand; LoF, loss-of-function; M, million; MEI, mobile element insertions.
