Fig 1.
(a) Each point represents the approximate geographic origin of the 76 individuals, and the number in the legend indicates the number of samples per indigenous group. Legend separates individuals from Northern (N), Central (C) and Southern (S) regions. For the exact GPS coordinates see S1 Table in S2 Material. (b) Total variants (M = millions) for each of the 76 individuals; the y axis enumerates the sampled individuals and is shared with panels c, d, and e; shape and color of the points correspond to the indigenous groups in the map. (c) Number of singletons (K = thousands) for each sample inferred from worldwide comparison with gnomAD and the 1000 Genomes Project. (d) Number of novel variants (K = thousands) not registered in dbSNP b152. (e) Percentage of Native American ancestry.
Fig 2.
Summary of variant effect annotations in the NM catalog.
All plots depict log10 number of variants. The color legend is shared between panels. (a) Consequences from the full set of SNVs. (b) Consequences from the full set of indels. (c) Consequences in natural selection signals. (d) Consequences in novel SNVs found at an allele frequency > 5%. nc-transcript = noncoding transcript.
Table 1.
NM whole genome variation summary.
Fig 3.
GRCh38 variation overview in NM.
(a) SNVs under selection, health related selection signals (matching a GWAS catalog or ClinVar registry) are highlighted in orange. (b) Novel SNVs with allele frequency higher than 5%. (c) SNVs altering enhancer or promoter elements. Height of the dots in a, b and c depicts the allele frequency of the variants. (d) Population-wide variant density. (e) Average NGS genome coverage.
Table 2.
Heterozygosity ratio and haplotype block length per population.
Fig 4.
(a) PCA of NM including 4 Native Peruvians (NP). (b) Summarized Parallel Coordinate Plot, showing only statistically significant PCs; (b) top panel, PC values per region, solid lines depict mean values, and dashed lines depict standard deviation; (b) bottom panel, dotted parallel coordinate plot, each dot depicts an individual. (c) ADMIXTURE analysis for different k, samples are ordered by geographic latitude and ethnic group. (d) Neighbor-joining tree based on FST between the 27 NM groups and NP in our study; colors indicate Region from Fig 4B.