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Please upload your data through the Browse button. The file must be separated by semicolons and weigh less than 1 Mb, in case of greater weight please upload a compressed version of the file (.zip, .tar or .tar.gz). This file should contain the following columns:
1.- acom_name: Name of the region from which the samples are collected
2.- collection_date: Date of collection of the sample with the format year/month/day (2021/04/25)
And at least one of the following columns:
3.- NCClade: Nextclade variant annotation
4.- pangolin_lineage: Pango annotation
5.- GISAID_clade: Annotation in GISAID format
6.- who: World Healt Organization variant annotation
Region for left and right plots
This section allows a comparative exploration of the evolution of the different variants of SARS-CoV-2 (CoV-19) between regions. Specifically, the graphs at the top give a more general view showing the total number of sequences or the frequency (stack or fill option respectively) of each variant over time in intervals of weeks. On the other hand, the bottom graphs show the evolution of the frequency of a single variant selected using the “Pick Variant” panel.
For a correct interpretation it is necessary to take into account:
• Sampling may not be uniform within the different autonomous communities. Therefore, it is important not to assume that the counts/frequencies shown are necessarily representative of the region.
• In relation with the last consideration, last data pints often has incomplete data and may change as more sequences come in.
Pick Variant Annotation:
SARS-CoV-2 (hCoV-19) genome sequences obtained from samples are classified into groups according their similarity in terms of mutations or groups of mutations. In myData CovidTag you can use four classification systems including the clades designed by GISAID, NextClade, Pangolin and the World Health Organization (WHO). For instance, the variant of interest 'VUI202012/01' first identified in the United Kindom in December 2020, is designated by GISAID as clade 'GRY', as 501Y.V1 by NextClade , as B.1.1.7 by Pango lineages and as 'Alpha' by WHO annotation.
You can select any of the variants using the drop-down menu for a brief description and a link to access complete information.
Pick y-axis transfomation:
Francesc Català Moll
Marc Noguera i Julian
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