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. 2017 Apr 3;18:61. doi: 10.1186/s13059-017-1181-7

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© The Author(s). 2017

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 1 — Functional impact of Neandertal non-synonymous alleles. Left: Average PolyPhen2 scores for archaic non-synonymous alleles in East Asians, South Asians, and Europeans (red squares). These averages are compared to averaged Polyphen2 scores for 1000 frequency matched sets of non-archaic non-synonymous alleles (yellow, orange, and brown violin plots). Polyphen2 scores range from 0–1 with higher scores associated with increased deleteriousness. Right: Average SIFT scores for archaic non-synonymous alleles in East Asians, South Asians, and Europeans (red squares). These averages are compared to averaged SIFT scores for 1000 frequency matched sets of non-archaic non-synonymous alleles (yellow, orange, and brown violin plots). SIFT scores range from 0–1 with lower scores associated with increased deleteriousness