first web update after 24A-C add

hodcroftlab · Jul 21, 2024 · 59a8284 · 59a8284
1 parent 5aaf647
commit 59a8284
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Showing 30 changed files with 54,867 additions and 12,676 deletions.
diff --git a/web/public/data/clusters.json b/web/public/data/clusters.json
@@ -14590,6 +14590,148 @@
         "Omicron"
       ]
     },
+    {
+      "alt_display_name": [
+        "JN.1"
+      ],
+      "aquaria_urls": [],
+      "build_name": "24A.Omicron",
+      "cluster_data": [],
+      "col": "#29a4ef",
+      "country_info": [],
+      "display_name": "24A (Omicron)",
+      "graphing": true,
+      "has_no_page": true,
+      "important": true,
+      "mutations": {
+        "nonsynonymous": [],
+        "synonymous": []
+      },
+      "nextstrain_build": true,
+      "nextstrain_name": "24A",
+      "nextstrain_url": "https://nextstrain.org/groups/neherlab/ncov/24A.Omicron",
+      "old_build_names": [],
+      "pango_lineages": [
+        {
+          "name": "JN.1",
+          "url": "https://cov-lineages.org/lineage.html?lineage=JN.1"
+        }
+      ],
+      "parent": "23I",
+      "snps": [
+        3565,
+        18894,
+        22926,
+        27810
+      ],
+      "snps_with_base": [
+        "T3565C",
+        "C18894T",
+        "T22926C",
+        "T27810C"
+      ],
+      "type": "variant",
+      "use_pango": true,
+      "who_name": [
+        "Omicron"
+      ]
+    },
+    {
+      "alt_display_name": [
+        "JN.1.11.1"
+      ],
+      "aquaria_urls": [],
+      "build_name": "24B.Omicron",
+      "cluster_data": [],
+      "col": "#6829ef",
+      "country_info": [],
+      "display_name": "24B (Omicron)",
+      "graphing": true,
+      "has_no_page": true,
+      "important": true,
+      "mutations": {
+        "nonsynonymous": [],
+        "synonymous": []
+      },
+      "nextstrain_build": true,
+      "nextstrain_name": "24B",
+      "nextstrain_url": "https://nextstrain.org/groups/neherlab/ncov/24B.Omicron",
+      "old_build_names": [],
+      "pango_lineages": [
+        {
+          "name": "JN.1.11.1",
+          "url": "https://cov-lineages.org/lineage.html?lineage=JN.1.11.1"
+        }
+      ],
+      "parent": "24A",
+      "snps": [
+        7113,
+        17334,
+        22928,
+        24872,
+        27810
+      ],
+      "snps_with_base": [
+        "7113T",
+        "17334T",
+        "22928C",
+        "24872T",
+        "27810C"
+      ],
+      "type": "variant",
+      "use_pango": true,
+      "who_name": [
+        "Omicron"
+      ]
+    },
+    {
+      "alt_display_name": [
+        "KP.3"
+      ],
+      "aquaria_urls": [],
+      "build_name": "24C.Omicron",
+      "cluster_data": [],
+      "col": "#331eee",
+      "country_info": [],
+      "display_name": "24C (Omicron)",
+      "graphing": true,
+      "has_no_page": true,
+      "important": true,
+      "mutations": {
+        "nonsynonymous": [],
+        "synonymous": []
+      },
+      "nextstrain_build": true,
+      "nextstrain_name": "24C",
+      "nextstrain_url": "https://nextstrain.org/groups/neherlab/ncov/24C.Omicron",
+      "old_build_names": [],
+      "pango_lineages": [
+        {
+          "name": "KP.3",
+          "url": "https://cov-lineages.org/lineage.html?lineage=KP.3"
+        }
+      ],
+      "parent": "24B",
+      "snps": [
+        7113,
+        17334,
+        22928,
+        24872,
+        27810
+      ],
+      "snps_with_base": [
+        "7113T",
+        "17334T",
+        "22928C",
+        "24872T",
+        "27810C"
+      ],
+      "type": "variant",
+      "use_pango": true,
+      "who_name": [
+        "Omicron"
+      ]
+    },
     {
       "alt_display_name": [
         "21A/S:154K"

diff --git a/web/public/data/mutationCounts/20A.EU1.json b/web/public/data/mutationCounts/20A.EU1.json
@@ -1,10 +1,10 @@
 {
   "S": {
-    "total": 168464,
+    "total": 168465,
     "counts": [
       {
         "mut": "S:D614G",
-        "count": 168377
+        "count": 168378
       },
       {
         "mut": "S:L18F",
@@ -45,11 +45,11 @@
     ]
   },
   "others": {
-    "total": 168464,
+    "total": 168465,
     "counts": [
       {
         "mut": "ORF1b:P314L",
-        "count": 168317
+        "count": 168318
       },
       {
         "mut": "N:P365S",

diff --git a/web/public/data/mutationCounts/20A.EU2.json b/web/public/data/mutationCounts/20A.EU2.json
@@ -1,10 +1,10 @@
 {
   "S": {
-    "total": 39274,
+    "total": 39275,
     "counts": [
       {
         "mut": "S:D614G",
-        "count": 39254
+        "count": 39255
       },
       {
         "mut": "S:H655Y",
@@ -45,19 +45,19 @@
     ]
   },
   "others": {
-    "total": 39274,
+    "total": 39275,
     "counts": [
       {
         "mut": "ORF1b:P314L",
-        "count": 39243
+        "count": 39244
       },
       {
         "mut": "ORF1a:M3087I",
-        "count": 39232
+        "count": 39233
       },
       {
         "mut": "ORF3a:Q57H",
-        "count": 39198
+        "count": 39199
       },
       {
         "mut": "ORF7a:T14I",

diff --git a/web/public/data/mutationCounts/20A.S.126A.json b/web/public/data/mutationCounts/20A.S.126A.json
@@ -1,6 +1,6 @@
 {
   "S": {
-    "total": 1399,
+    "total": 1406,
     "counts": [
       {
         "mut": "S:A845S",
@@ -45,11 +45,11 @@
     ]
   },
   "others": {
-    "total": 1399,
+    "total": 1406,
     "counts": [
       {
         "mut": "ORF7b:L14-",
-        "count": 1335
+        "count": 1342
       },
       {
         "mut": "ORF1a:T1567I",

diff --git a/web/public/data/mutationCounts/20I.Alpha.V1.json b/web/public/data/mutationCounts/20I.Alpha.V1.json
@@ -1,6 +1,6 @@
 {
   "S": {
-    "total": 1124313,
+    "total": 1124339,
     "counts": [
       {
         "mut": "S:K1191N",
@@ -12,7 +12,7 @@
       },
       {
         "mut": "S:S98F",
-        "count": 20830
+        "count": 20833
       },
       {
         "mut": "S:W152R",
@@ -24,7 +24,7 @@
       },
       {
         "mut": "S:L18F",
-        "count": 7585
+        "count": 7586
       },
       {
         "mut": "S:I68-",
@@ -37,19 +37,19 @@
     ]
   },
   "others": {
-    "total": 1124313,
+    "total": 1124339,
     "counts": [
       {
         "mut": "ORF8:K68*",
-        "count": 400195
+        "count": 400217
       },
       {
         "mut": "ORF1b:K1383R",
-        "count": 230912
+        "count": 230913
       },
       {
         "mut": "ORF1b:P218L",
-        "count": 154994
+        "count": 154999
       },
       {
         "mut": "N:G204P",
@@ -61,19 +61,19 @@
       },
       {
         "mut": "ORF1a:Q3966R",
-        "count": 64494
+        "count": 64495
       },
       {
         "mut": "ORF1a:M2259I",
-        "count": 61025
+        "count": 61024
       },
       {
         "mut": "ORF3a:W131C",
-        "count": 53018
+        "count": 53021
       },
       {
         "mut": "ORF1b:P1975S",
-        "count": 44675
+        "count": 44681
       },
       {
         "mut": "ORF1a:F2780L",

diff --git a/web/public/data/mutationCounts/20J.Gamma.V3.json b/web/public/data/mutationCounts/20J.Gamma.V3.json
@@ -1,6 +1,6 @@
 {
   "S": {
-    "total": 120279,
+    "total": 120291,
     "counts": [
       {
         "mut": "S:P681H",
@@ -20,7 +20,7 @@
       },
       {
         "mut": "S:Q675H",
-        "count": 1346
+        "count": 1349
       },
       {
         "mut": "S:L5F",
@@ -45,15 +45,15 @@
     ]
   },
   "others": {
-    "total": 120279,
+    "total": 120291,
     "counts": [
       {
         "mut": "ORF9b:Q77E",
-        "count": 119630
+        "count": 119642
       },
       {
         "mut": "ORF1a:S2947N",
-        "count": 20919
+        "count": 20922
       },
       {
         "mut": "ORF1a:K3573R",
@@ -81,11 +81,11 @@
       },
       {
         "mut": "ORF1a:T1820I",
-        "count": 2691
+        "count": 2692
       },
       {
         "mut": "N:D402Y",
-        "count": 2589
+        "count": 2588
       }
     ]
   }