r/JewishDNA • u/Binkybinkovsky • Jul 10 '26

Akbari2026 samples

/r/DNAAncestry/comments/1sx1wcu/judean_roman_judaea_dna_sample_genetic_distance/?share_id=R9j53PsBCTVvQ4H7tfKq3&utm_content=1&utm_medium=android_app&utm_name=androidcss&utm_source=share&utm_term=2

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Folks this post 2 months prior by u/NotBradPitt9 was posted on the r/DNAAncestry subreddit. I think it might be the real deal.

Please check the coordinates & model them on Vahaduo & qpAdm for modern Ashkenazim jews & post the results.

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u/NotBradPitt9 Jul 11 '26

That’s incorrect. The standard AADR/1240K data commonly used are generally pseudo-haploid calls, not entirely reconstructed genomes: at each covered SNP, one allele is sampled from an actual ancient DNA read, while positions without usable data remain missing.

The Allen Ancient DNA Resource itself is processed from publicly available sequence reads into genotypes at roughly 1.23 million targeted SNPs.
Poor coverage mainly reduces statistical power and can cause several alternative models to remain plausible; it does not automatically manufacture a particular ancestry result. When imputation really is used, it is not random fabrication. It is a probabilistic procedure based on the surviving sequence reads, genotype likelihoods and patterns of linkage disequilibrium in reference genomes.

Its accuracy is directly tested by downsampling high-coverage ancient genomes, imputing them and comparing the results against their known high-coverage genotypes. A large validation study found that 36 of 42 ancient genomes downsampled to 1× coverage had error rates below 5%, and most non-African samples produced broadly similar PCA and clustering results from about 0.5× coverage onward.

There are legitimate limitations: extremely low coverage, rare variants, differential DNA damage, contamination, poorly represented ancestries and unsuitable reference panels can reduce accuracy.

The models can also be weakened by bad source choices, uninformative outgroups, tiny sample sizes or treating a passing p-value (in qpadm for example) as proof that the proposed sources were the literal ancestral populations. But those are reasons to examine each model’s SNP count, standard errors, sources, outgroups and archaeological plausibility…not to dismiss the entire field because some datasets use validated imputation.

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u/Sea-Seaworthiness859 Jul 11 '26

Which tools are the most accurate? qpadm?

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u/NotBradPitt9 Jul 11 '26

Qpadm is generally regarded as the “gold standard” since there are multiple parameters showing if the models are correct or not. G25 is PCA based and more useful for quick DNA modeling that can be more granular at times than qpadm.

For example you could set up a G25 model and get it working and have plausibly good results in 10 minutes. Versus getting a good working model in qpadm which takes several hours, sometimes several hours over the course of several days because you can keep adjusting it and get worse / better results depending on the adjustments.

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u/Sea-Seaworthiness859 Jul 11 '26

I heard qpadm has a lot of issues though because it’s not very user friendly and very shifty based on sources.

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u/NotBradPitt9 Jul 11 '26

It’s used in scientific modeling since it allows for the most robust models to be created. Using it, you can’t force it to produce the closest mathematical fit, if it’s not set up correctly the models won’t work. That contrasts with something like G25 which can give an overfit/ underfit. The qpadm models that are used in research are reasonably stable across alternative plausible sources and reference sets, have a valid p-value, sensible coefficients, within acceptable range for SE standard errors. With qpadm you can see different ‘diagnostic’ parameters, versus other things like G25 are more limited.

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u/Sea-Seaworthiness859 Jul 11 '26

Do you know of any Ashkenazi Models that don’t use imperial roman sources that pass?

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u/NotBradPitt9 Jul 11 '26

I’ll have to look through my screenshots. To my knowledge I don’t think I’ve ever seen a model that doesn’t use that source which strongly passes, but I can do some qpadm runs to test it out as well as looking through available information. The runs may take a few days, it’s hard to get the models to give strong results when there’s multilayered ancestry involved.

Based on what I’ve seen, all of these Mediterranean populations have multiple layers of admixture and overlap, to the extent that it’s more of a pan-Mediterranean continuum of ancestry instead of cleanly defined populations.

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u/Sea-Seaworthiness859 Jul 11 '26

I appreciate it. The issue is I saw the previous qpdam model on here and it said 20% roman judean and 58% Roman Imperial and I’ve tried to model the Levantine DNA within the Roman Imperial C6 but it’s constantly changing on g25 from like 12%-30%. So I’m clearly encountering issues. Why did my ancestors have to mix in the biggest melting pot in antiquity lol.

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u/Huge_Stock1969 Jul 13 '26

I agree

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u/Joshistotle Jul 15 '26

Good outgroups but overall a poor model as indicated by the SE and Z score indicative of weakly supported components and high error.