-
Notifications
You must be signed in to change notification settings - Fork 17
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #43 from cov-lineages/update_omicron
Update omicron
- Loading branch information
Showing
6 changed files
with
210 additions
and
104 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| _program = "constellations" | ||
| __version__ = "v0.0.27" | ||
| __version__ = "v0.0.28" | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| { | ||
| "label": "Omicron (BA.1-like)", | ||
| "description": "BA.1 lineage defining mutations", | ||
| "sources": [ | ||
| ], | ||
| "type": "variant", | ||
| "variant": { | ||
| "Pango_lineages": [ | ||
| "BA.1" | ||
| ], | ||
| "WHO_label": "Omicron", | ||
| "mrca_lineage": "BA.1", | ||
| "lineage_name": "BA.1", | ||
| "parent_lineage": "B.1.1.529", | ||
| "representative_genome": "" | ||
| }, | ||
| "tags": [ | ||
| "BA.1" | ||
| ], | ||
| "sites": [ | ||
| "orf1ab:K856R", | ||
| "del:6513:3 # orf1a:SL2083I ", | ||
| "nuc:T5386G", | ||
| "orf1ab:A2710T", | ||
| "# nuc:G11287T # orf1ab:L3674F # aligners often place the parent del at 11283 rather than 11288", | ||
| "orf1ab:I3758V", | ||
| "nuc:C15240T", | ||
| "spike:A67V", | ||
| "del:21765:6 # spike:HV69-", | ||
| "spike:T95I", | ||
| "del:21987:9 # spike:VYY143-", | ||
| "del:22194:3 # spike:NL211I", | ||
| "nuc:22205+GAGCCAGAA # spike:-215EPE", | ||
| "spike:S371L", | ||
| "spike:G446S", | ||
| "spike:G496S", | ||
| "spike:T547K", | ||
| "spike:N856K", | ||
| "spike:L981F", | ||
| "m:D3G" | ||
| ], | ||
| "note": "Unique mutations for sublineage", | ||
| "note2": "Requires ancestral mutation so scorpio tie breaks correctly", | ||
| "rules": { | ||
| "min_alt": 10, | ||
| "max_ref": 3, | ||
| "spike:D614G": "not ref" | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| { | ||
| "label": "Probable Omicron (BA.1-like)", | ||
| "description": "BA.1 lineage defining mutations with lower thresholds to handle lower quality consensus sequences", | ||
| "sources": [ | ||
| ], | ||
| "type": "variant", | ||
| "variant": { | ||
| "Pango_lineages": [ | ||
| "BA.1" | ||
| ], | ||
| "WHO_label": "Omicron", | ||
| "mrca_lineage": "BA.1", | ||
| "representative_genome": "" | ||
| }, | ||
| "tags": [ | ||
| "BA.1" | ||
| ], | ||
| "sites": [ | ||
| "nuc:C3037T # B.1 defining", | ||
| "orf1ab:T3255I", | ||
| "orf1ab:P3395H", | ||
| "orf1ab:SGF3675- # del:11288:9", | ||
| "nuc:T13195C", | ||
| "orf1ab:P4715L # B.1 defining", | ||
| "orf1ab:I5967V", | ||
| "spike:G142D", | ||
| "spike:G339D", | ||
| "spike:S373P", | ||
| "spike:S375F", | ||
| "spike:K417N", | ||
| "spike:N440K", | ||
| "spike:S477N", | ||
| "spike:T478K", | ||
| "spike:E484A", | ||
| "spike:Q493R", | ||
| "spike:Q498R", | ||
| "spike:N501Y", | ||
| "spike:Y505H", | ||
| "spike:D614G # B.1 defining", | ||
| "spike:H655Y", | ||
| "spike:N679K", | ||
| "spike:P681H", | ||
| "spike:N764K", | ||
| "spike:D796Y", | ||
| "spike:Q954H", | ||
| "spike:N969K", | ||
| "nuc:C25000T", | ||
| "nuc:C25584T", | ||
| "e:T9I", | ||
| "m:Q19E", | ||
| "m:A63T", | ||
| "nuc:A27259C", | ||
| "nuc:C27807T", | ||
| "nuc:A28271T", | ||
| "n:P13L", | ||
| "del:28362:9 # n:ERS31-", | ||
| "n:RG203KR # B.1.1 defining", | ||
| "orf1ab:K856R # BA.1 defining", | ||
| "del:6513:3 # orf1a:SL2083I # BA.1 defining", | ||
| "nuc:T5386G # BA.1 defining", | ||
| "orf1ab:A2710T # BA.1 defining", | ||
| "orf1ab:I3758V # BA.1 defining", | ||
| "nuc:C15240T # BA.1 defining", | ||
| "spike:A67V # BA.1 defining", | ||
| "del:21765:6 # spike:HV69- # BA.1 defining", | ||
| "spike:T95I # BA.1 defining", | ||
| "del:21987:9 # spike:VYY143- # BA.1 defining", | ||
| "del:22194:3 # spike:NL211I # BA.1 defining", | ||
| "nuc:22205+GAGCCAGAA # spike:-215EPE # BA.1 defining", | ||
| "spike:S371L # BA.1 defining", | ||
| "spike:G446S # BA.1 defining", | ||
| "spike:G496S # BA.1 defining", | ||
| "spike:T547K # BA.1 defining", | ||
| "spike:N856K # BA.1 defining", | ||
| "spike:L981F # BA.1 defining", | ||
| "m:D3G # BA.1 defining" | ||
| ], | ||
| "note": "This file has been added to allow probable calls to be made, even when the incoming consensus pipeline calls for ref in lower quality regions", | ||
| "rules": { | ||
| "min_alt": 25, | ||
| "max_ref": 18 | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| { | ||
| "label": "BA.2-like", | ||
| "description": "BA.2 lineage defining mutations", | ||
| "sources": [ | ||
| ], | ||
| "type": "variant", | ||
| "variant": { | ||
| "Pango_lineages": [ | ||
| "BA.2" | ||
| ], | ||
| "mrca_lineage": "BA.2", | ||
| "lineage_name": "BA.2", | ||
| "parent_lineage": "B.1.1.529", | ||
| "representative_genome": "" | ||
| }, | ||
| "tags": [ | ||
| "BA.2" | ||
| ], | ||
| "sites": [ | ||
| "orf1ab:S135R", | ||
| "orf1ab:T842I", | ||
| "orf1ab:G1307S", | ||
| "nuc:C4321T", | ||
| "orf1ab:L3027F", | ||
| "nuc:A9424G", | ||
| "orf1ab:T3090I", | ||
| "orf1ab:L3201F", | ||
| "nuc:C10198T", | ||
| "nuc:G10447A", | ||
| "nuc:C15714T", | ||
| "nuc:C12880T", | ||
| "nuc:C15714T", | ||
| "orf1ab:R5716C", | ||
| "orf1ab:T6564I", | ||
| "nuc:A20055G", | ||
| "spike:T19I", | ||
| "del:21633:9 # spike:LPPA24S", | ||
| "nuc:T22200G # spike:V231G # but this seems to be wrong aa ref allele", | ||
| "spike:S371F", | ||
| "spike:T376A", | ||
| "spike:D405N", | ||
| "spike:R408S", | ||
| "nuc:C26060T # orf3a:T233I # but this seems to be wrong aa ref allele", | ||
| "nuc:C26858T", | ||
| "orf6:D61L # GAT->CTC", | ||
| "n:S413R" | ||
| ], | ||
| "note": "Unique mutations for sublineage", | ||
| "rules": { | ||
| "min_alt": 19, | ||
| "max_ref": 3 | ||
| } | ||
| } |