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. 2019 Jan 24;11:15. doi: 10.1186/s13148-019-0615-3

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© The Author(s). 2019

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. 2 — Detecting what is not supposed to be there. Call rates of Y-chromosome probes among the 1442 female samples for three approaches to classifying detected probes. Probes are ordered on the x-axis by increasing call rate (order not identical between curves). Only six probes had a call rate < 2% when using the conventional cut-off of 0.01 with the background distribution estimated from negative control probes (NEG/0.01). For more stringent criteria (NSP/0.1 and NEG/1e−40), there is an almost clear-cut separation between undetected and detected probes including some cross-hybridizing to autosomal CpG sites