Amino acid missense, deletion, or insertion mutations across all samples. Sorted by count of mutation, use dropdown to sort by genomic position. Nucleotide level variants may be repeated where there are multiple AA changes associated with a single genomic event. A table summarising nucleotide level variants can be found here.

Summary heatmap of all residue positions for which there is at least one mutation across all samples. Individual sample IDs and mutations are plotted on datapoint, for large samples sets these become visible at higher zoom levels. Residues are labelled in the following format: sample_id(pango_lineage):mutation. Hover text will show z: selected score for sample-residue and sample ID and mutation. For a description of these scores see Table 3 in the SPEAR README. For a full screen view of the current plot see here, and for a fullscreen heatmap across all residues (easier comparison between reports), see here.

Summarised scores per sample (sum across sample), cells with values higher than selected baseline are highlighted. Selected baseline is always shown in the top row, table is sorted by the cm mAb escape all classes sum column by default, the drop down can be used to sort on other scores. For a description of these scores see Table 4 in the SPEAR README. For a full screen view of this table see here. Source data used to produce this table can be found in the file spear_score_summary.tsv
Quality warnings: ! - Spike N contig (default 150nt) ; ^ - Spike RBD N content (default 12nt) ; * - Global N percentage (default > half N percentage cutoff) ; # - Spike N percentage (default > 5%)

Table of mutation counts in protein domains. Total mutations: the total number of mutations in this domain seen across all samples. Unique mutations: total number of unique residue mutations observed across all samples. A full table of protein domain mutation in each sample can be found here and in spear_annotation_summary.tsv

Table of mutation counts of protein features (in domains). Total mutations: the total number of mutations in this feature seen across all samples. Unique mutations: total number of unique residue mutations observed across all samples in this feature. A full table of protein feature mutation in each sample can be found here and in spear_annotation_summary.tsv

Table of mutated residues with other residue interactions, and their interaction type e.g. H-bond, salt-bridge, "contact". A full table of interacting residue mutations in each sample can be found here and in spear_annotation_summary.tsv

Subset of feature table containing mutations in Spike residues 675-695, the region of the S1/S2 furin cleavage site. A full table of furin site mutations in each sample can be found here and in spear_annotation_summary.tsv

Mutations in Spike NTD. A full table of NTD mutations in each sample can be found here and in spear_annotation_summary.tsv