Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic
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SciScore for 10.1101/2020.08.03.234005: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Functional annotation of the mutations was performed using the standard protocol of ANNOVAR ([25] and https://doc-openbio.readthedocs.io/projects/annovar/en/latest/) based on the genome annotations in GenBank entry NC_045512.2 Out of 251,481 mutations initially called in 32,115 isolates, 251,273 were retained after removing redundant DNA symbols (anything but A,C,G,T) as well as mutation calls separated by less than 20 nt from either end of the reference, of which 243,454 were SNVs in 32070 isolates. ANNOVARsuggested: (ANNOVAR, RRID:SCR_012821)The *RNAfold.txt files were used to add a … SciScore for 10.1101/2020.08.03.234005: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Functional annotation of the mutations was performed using the standard protocol of ANNOVAR ([25] and https://doc-openbio.readthedocs.io/projects/annovar/en/latest/) based on the genome annotations in GenBank entry NC_045512.2 Out of 251,481 mutations initially called in 32,115 isolates, 251,273 were retained after removing redundant DNA symbols (anything but A,C,G,T) as well as mutation calls separated by less than 20 nt from either end of the reference, of which 243,454 were SNVs in 32070 isolates. ANNOVARsuggested: (ANNOVAR, RRID:SCR_012821)The *RNAfold.txt files were used to add a stem-loop annotation column “RNAfold” to all MAF files using the vlookup function in Excel and saved as a tab delimited text file. Excelsuggested: NoneResults from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
- No funding statement was detected.
- No protocol registration statement was detected.
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