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. 2019 Apr 15;9:6095. doi: 10.1038/s41598-019-42640-w

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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LipY764 Assembly. (a) Assembly step: whole genome NGS reads from males (blue) are mapped to Y-specific bait sequences (black). Mapped reads (dark blue) are then extracted and assembled (grey). Classification step: the assembly is shown in grey with hatchmarks representing 50 bp windows. Male (blue) and female (red) reads are mapped to the assembly and mapping coverages normalised to autosomal coverages per window were estimated. The probability of Y- or nonMSY-specificity per window is obtained by comparing normalised coverages in males and females. class nonMSY: XX/XY/AUT ≈ 1 in males and ≈ 1 in females; class Y: scY ≤ 1 in males and ≈ 0 in females, mcY > 1 in males and ≈ 0 in females. (b) Frequency distribution of normalised mapping coverage in classY windows. The cut-off scY to seperate mcY is set to 1 (red dashed line). (c) Resulting statistics for the assembly and classification approach. (d) Position of LipY764 contigs on eMSYv3⁴⁶ (data in Supplementary Table S5). Contigs having a single unique position on eMSYv3 are shown in grey, contigs with multiple hits in black/bold.