- 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. -
-+ 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. +
+- 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. -
-+ 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. +
+- 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. -
-+ 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 mutation filters can be provided by adding one mutation after the other. -
-+ Multiple mutation filters can be provided by adding one mutation after the + other. +
+- To filter for any mutation at a given position you can omit the <base>. -
-- 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. -
++ To filter for any mutation at a given position you can omit the{' '} + <base>. +
++ 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. +