Variation of Genomic Sites Associated with Severe Covid-19 Across Populations: Global and National Patterns
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SciScore for 10.1101/2020.11.22.20236414: (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 The pooling procedure included i) standard filtering in PLINK [10] (geno 0.05, maf 0.01, mind 0.1, pruning indep-pairwise 1500 150 0.2), ii) running the set of PCAs by smartpca software [11], [12], and iii) identifying groups of populations with homogeneity within the groups but pronounced variation between the groups; we omitted some populations which could not stand alone because of the low sample size and could not be pooled because of their genetic peculiarities; the details of this pooling procedure are described in [13]. PLINKsuggested: (PLINK, RRID:SCR_001757)Imputing was done by … SciScore for 10.1101/2020.11.22.20236414: (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 The pooling procedure included i) standard filtering in PLINK [10] (geno 0.05, maf 0.01, mind 0.1, pruning indep-pairwise 1500 150 0.2), ii) running the set of PCAs by smartpca software [11], [12], and iii) identifying groups of populations with homogeneity within the groups but pronounced variation between the groups; we omitted some populations which could not stand alone because of the low sample size and could not be pooled because of their genetic peculiarities; the details of this pooling procedure are described in [13]. PLINKsuggested: (PLINK, RRID:SCR_001757)Imputing was done by the Beagle software [30] by 200 iterations, using 1000 Genomes project dataset as a reference. Beaglesuggested: (BEAGLE, RRID:SCR_001789)1000 Genomessuggested: (1000 Genomes Project and AWS, RRID:SCR_008801)Cartographic analysis: The maps of the geographic distribution of the two COVID-associated markers were constructed using the GeneGeo software [31], [32]. GeneGeosuggested: NoneTo estimate the differences in allele frequencies between groups the Fisher’s exact test was used using the application of GraphPad InStat software package (GraphPad Software, San Diego, CA, USA); the differences were considered statistically significant at p<0.05 with the Bonferroni correction. GraphPad InStatsuggested: (GraphPad, RRID:SCR_000306)GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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