PSET SARS-CoV-2 Supplement

Table S1. Variation. Variant counts and percentages are listed by position and type together with reference and alternate allele. Table S2. Regional Mutation Frequency. The number of mutations by position are listed by position and region type (assay or non-assay. Table S3. Regional Mutation Percentage. The percentage of positions with a given number of mutations is listed for assay and non-assay regions. Table S4. Confusion Matrix. For each assay, the confusion matrix categorizes sequence alignment results by assay according to the workflow rules. Table S5. Near Neighbor Analysis. This is the confusion matrix for each assay according to a previous workflow described on virological.org that looked at off-target species. Table S6. Variant Call Date. This table lists the date of VoC or VoI designation by each disease control center. Table S7. Assay Escape Count. The first column lists the FN count associated with the total number of sequences listed in the second column. Table S8. Predicted Shared Failure. This table lists the number of times an assay was observed failing with n other assays. In other words, the numeric column names represent the number of other assays that failed for a given sequence with the assay in the id column.

表S1 变异情况。本表格按变异位点与变异类型列出变异计数与占比，并附带参考等位基因与变异等位基因信息。
表S2 区域突变频率。本表格按突变位点与区域类型（检测区域或非检测区域）列出各区域的突变数量。
表S3 区域突变占比。本表格针对检测区域与非检测区域，列出携带特定突变数量的位点占比。
表S4 混淆矩阵（Confusion Matrix）。针对每项检测方法，本混淆矩阵依据工作流规则，按检测方法对序列比对结果进行分类。
表S5 近邻分析（Near Neighbor Analysis）。本表格基于virological.org平台发布的既往工作流，针对每项检测方法生成混淆矩阵，用于分析脱靶物种。
表S6 变异检出日期。本表格列出各疾病预防控制中心公布的关注变异株（Variant of Concern, VoC）与待关注变异株（Variant of Interest, VoI）的指定日期。
表S7 检测方法逃逸计数。首列列出与第二列所列总序列数相关的假阴性（False Negative, FN）计数。
表S8 预测共同失效情况。本表格列出某检测方法与n项其他检测方法共同失效的观测次数。换言之，表格的数值型列名代表：当某序列与id列对应的检测方法同时失效时，同步失效的其他检测方法的数量。