message: check whether a position was sequenced can called when calculating distance
diff: @@ -93,9 +93,22 @@ export function calculate_distance(node: AuspiceTreeNodeExtended, seq: AnalysisR
  }
  }
  }
  + let undetermined_sites = 0
  + if (node.mutations) {
  + for (const nmut of node.mutations) {
  + const pos = nmut[0]
  + if (
  + pos < seq.alignmentStart ||
  + pos >= seq.alignmentEnd ||
  + !seq.missing.every((d) => pos < d.begin && pos >= d.end)
  + ) {
  + undetermined_sites += 1
  + }
  + }
  + }
  const numMut = node.mutations?.size ?? 0
  - return numMut + seq.substitutions.length - 2 * shared_differences - shared_sites
  + return numMut + seq.substitutions.length - 2 * shared_differences - shared_sites - undetermined_sites
  }
  export function get_differences(node: AuspiceTreeNodeExtended, seq: AnalysisResult, root_seq: string) {
  