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. 2019 Jul 17;9:10383. doi: 10.1038/s41598-019-46875-5

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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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Comparison of genome and CpG coverage at different minimum depths and nucleotide amplification bias between NovaSeq and HiSeq X sequencing platforms. (a) CpG site coverage at different minimum depths (1–80x). Loess smoothing was applied, with the 95% confidence intervals indicated by gray shaded areas. (b) Nucleotide amplification biases, expressed as the logarithm 2 transformed ratio of observed to expected coverage for different nucleotide and dinucleotide combinations. G/C-rich category (defined as C, G, CC, CG, GC and GG) and A/T-rich category (defined as A, AA, AT, T, TA and TT) are highlighted in pink. Each line represents one sample (library). (c) Genome coverage at each minimum depth across different number of raw read pairs. (d) CpG site coverage at each minimum depth across different number of raw read pairs. For c and d, results obtained from downsampling analyses are shown here for minimum depths ranging from 1–200x for library sizes consisting of 100–4000 M raw read pairs. All available samples were pooled for the downsampling analyses. n.s.: not statistically significant, P > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001. Bars show average values, with error bars representing standard error of mean.