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. 2021 Aug 10;11:16194. doi: 10.1038/s41598-021-95435-3

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© The Author(s) 2021

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Defining IR and the positive slope region for screening a termination site. (a) A plot showing the cumulative distribution of the reads in and around an IR in S. aureus Newman, NCBI ID: NC_009641, RNA-seq ID: ERR1337989 for operon: [3686,9675,10900], where 3686–9675 is the coding region and 9675–10,900 is the IR marked by red lines. The blue curve shows the cumulative frequency of RNA-seq reads at each position in the above-mentioned operon. The numbers on the x-axis represent the actual genome coordinates. (b) The IR region for operon where slopes have been calculated from cumulative frequency values in a) using a window of 10 bases. A region of positive slope implies an increase in reads frequency after the previous drop. Red lines approximately mark the start and end of the IR (IR^start and IR^end). The green lines mark the start and end of the first positive slope region (pos^st and pos^end, respectively) of the curve, indicating the end of transcription should be before this first read-increase region. (c) The inset around the transcription termination region is shown schematically divided into three zones; Zone 1: stop codon to start of the positive slope region; Zone 2: start of the positive slope region to end of the positive slope region; Zone 3: end of the positive slope region to the end of the IR.