Exercise 7 of 17

Mutations within a lineage

Fixed training server

List the nucleotide mutations (on the 'main' sequence) that occur in at least 5% of sequences belonging to lineage B.1.1.7 including its sublineages. Return at most 20 rows.

The output should have this shape:

mutationFrom | mutationTo | position | sequenceName | proportion | coverage | count
------------ | ---------- | -------- | ------------ | ---------- | -------- | -----
A            | G          | 23403    | main         | 0.42       | 1200     | 504

Write a query and run it. The result is compared with the reference answer without considering row order.

Loading query editor…

Explanation

Filter the table to lineage B.1.1.7 and its sublineages. Then, use mutations to get changes on the main nucleotide sequence with a minimum proportion of 5% and keep the first 20.

lineage mutations aggregation

Reference answer

default
  .filter(pangoLineage.lineage('B.1.1.7', includeSublineages:=true))
  .mutations(minProportion:=0.05, sequenceNames:={main})
  .limit(20)