+
+ Mutation Search
+
+
+
+
+ Nucleotide Mutations and Insertions
+
+
+ For a single-segmented organism, nucleotide mutations have the format{' '}
+ <position><base> or{' '}
+ <base_ref><position><base>. A <base>{' '}
+ can be one of the four nucleotides A, T, C, and{' '}
+ G. It can also be - for deletion and N for unknown. For
+ example if the reference sequence is A at position 23 both:{' '}
+ 23T and A23T will yield the same results.
+
+
+ If your organism is multi-segmented you must append the name of the segment
+ to the start of the mutation, e.g. S:23T and S:A23T for a
+ mutation in segment S.
+
+
+ Insertions can be searched for in the same manner, they just need to have{' '}
+ ins_ appended to the start of the mutation. Example{' '}
+ ins_10462:A or if the organism is multi-segmented{' '}
+ ins_S:10462:A.
+
+
+
+ Amino Acid Mutations and Insertions
+
+
+ An amino acid mutation has the format{' '}
+ <gene>:<position><base> or{' '}
+ <gene>:<base_ref><position><base>. A{' '}
+ <base> can be one of the 20 amino acid codes. It can also be{' '}
+ - for deletion and X for unknown. Example: E:57Q.
+
+
+ Insertions can be searched for in the same manner, they just need to have{' '}
+ ins_
+ appended to the start of the mutation. Example ins_NS4B:31:N.
+
+
+
Insertion Wildcards
+
+ Loculus supports insertion queries that contain wildcards ?. For
+ example ins_S:214:?EP? will match all cases where segment S{' '}
+ has an insertion of EP between the positions 214 and 215 but also an
+ insertion of other AAs which include the EP, e.g. the insertion{' '}
+ EPE will be matched.
+
+
+ You can also use wildcards to match any insertion at a given position. For
+ example ins_S:214:?: will match any (but at least one) insertion
+ between the positions 214 and 215.
+
+
+
Multiple Mutations
+
+ Multiple mutation filters can be provided by adding one mutation after the
+ other.
+
+
+
Any Mutation
+
+ To filter for any mutation at a given position you can omit the{' '}
+ <base>.
+
+
+
No Mutation
+
+ You can write a . for the <base> to filter for sequences
+ for which it is confirmed that no mutation occurred, i.e. has the same base
+ as the reference genome at the specified position.
+
+