Supplementary table S1

Supplementary table S1 for the October 2024 preprint of "Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny".The columns are:In_may_2024_preprint. Whether or not this run was in the May 2024 preprint. The values are T for true or F for falseStudy, Sample, Experiment, Run, Platform, Country, Region, Collection_date, First_created. These are all directly from the ENA metadata.Run_count. The number of runs from the sample accessionDate_tree. A consensus date, using up 3 sources of data for each sample: COG-UK, GISAID, ENA/SRA. This was used for building the trees. Where dates conflicted for a given sample, the order of preference used was the date with highest resolution, then COG-UK, GISAID, and finally ENA/SRA.Date_tree_order. This helped define the order in which the samples were added to the tree. The tree was built in two main batches: the May 2024 preprint, and the October 2024 updated preprint. In all cases, only samples with Viridian_result. This is “PASS” if Viridian finished and made a consensus sequence, “NO_READS” if the reads failed to download, “FAIL_QC” if one of Viridian’s QC requirements was not met, or “FAIL_OTHER” if something else went wrong during processing.Genbank_accession. This is the GenBank accession of the assemblyGenbank_other_runs. Any other run accessions associated with the GenBank entry, other than that in the Run columnIn_Viridian_tree. “T” or “F” to indicate if the sample is in the viridian treeIn_intersection. “T” or “F” to indicate if the sample is in the intersection treeArtic_primer_version. If known, the ARTIC primer scheme from ENA metadataViridian_amplicon_scheme. Amplicon scheme called by ViridianViridian_N. Number of Ns in the viridian consensus sequence, after aligning to the reference with MAFFTGenbank_N. Number of Ns in the GenBank consensus sequence, after aligning to the reference with MAFFTViridian_pangolin/Viridian_scorpio. Pangolin/scorpio call from the Viridian consensus sequence, using pangolin data version 1.21Genbank_pangolin/Genbank_scorpio. Pangolin/scorpio call from the GenBank consensus sequence, using pangolin data version 1.21Genbank_tree_name. Name of the sample in the GenBank treeViridian_cons_len. Length of the Viridian consensus sequence Viridian_cons_het. Number of heterozyous (non-ACGTN) calls in the Viridian consensus sequenceViridian_pangolin_1.29/Viridian_scorpio_1.29. Pangolin/scorpio call from the Viridian consensus sequence, using pangolin data version 1.29