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Machine-Readable Reference File #163

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Machine-Readable Reference File #163

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107 changes: 107 additions & 0 deletions covariants_objects.json
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// 'alignment_defining' means searching these in alignment _should_ identify - but will miss reversions or incomplete coverage
// 'phylogenetic_defining' means on a phylogenetic tree these should identify the cluster
// 'build_name' is what the build is called in files & URLs (character safe)
// 'display name' is prettier for displaying in graphics/pages etc
// 'pango_name' may not be an exact match to Pango designation

{
"variants": [
{
"build_name": "S.501Y.V1",
"display_name": "20I/501Y.V1",
"pango_name": "B.1.1.7",
"nextstrain_url": "https://nextstrain.org/groups/neherlab/ncov/S.501Y.V1?c=gt-S_501",
"covariants_url": "https://covariants.org/variants/S.501Y.V1",
"color": "#b30000",
"defining_mutations": [
{
"type": "alignment_defining",
"mutations": [
"A23063T", //S N501Y
"C23604A", //S P681H
"G24914C" //S D1118H
]
},
{
"type": "phylogenetic_defining",
// these will be pulled directly from clades files & thus won't have reference base
"mutations": [
"8782C",
"14408T",
"23403G",
"28881A",
"28882A",
"23063T",
"14676T",
"15279T"
]
}
],
"all_mutations": [
//this is copied directly from clusters.py - NOT JSON FORMATTED
"nonsynonymous": [
{"gene": "S", "left": "H", "pos": 69, "right": "-"},
{"gene": "S", "left": "V", "pos": 70, "right": "-"},
{"gene": "S", "left": "Y", "pos": 144, "right": "-"},
{"gene": "S", "left": "N", "pos": 501, "right": "Y"},
{"gene": "S", "left": "A", "pos": 570, "right": "D"},
{'gene': 'S', 'left': 'D', 'pos': 614, 'right': 'G'},
{"gene": "S", "left": "P", "pos": 681, "right": "H"},
{'gene': 'S', 'left': 'T', 'pos': 716, 'right': 'I'},
{'gene': 'S', 'left': 'S', 'pos': 982, 'right': 'A'},
{'gene': 'S', 'left': 'D', 'pos': 1118, 'right': 'H'},
{'gene': 'ORF1a', 'left': 'T', 'pos': 1001, 'right': 'I'},
{'gene': 'ORF1a', 'left': 'A', 'pos': 1708, 'right': 'D'},
{'gene': 'ORF1a', 'left': 'I', 'pos': 2230, 'right': 'T'},
{"gene": "ORF1a", "left": "S", "pos": 3675, "right": "-"},
{"gene": "ORF1a", "left": "G", "pos": 3676, "right": "-"},
{"gene": "ORF1a", "left": "F", "pos": 3677, "right": "-"},
{'gene': 'N', 'left': 'D', 'pos': 3, 'right': 'L'},
{"gene": "N", "left": "R", "pos": 203, "right": "K"},
{"gene": "N", "left": "G", "pos": 204, "right": "R"},
{'gene': 'N', 'left': 'S', 'pos': 235, 'right': 'F'},
{'gene': 'ORF1b', 'left': 'P', 'pos': 314, 'right': 'L'},
{"gene": "ORF8", "left": "Q", "pos": 27, "right": "*"},
{'gene': 'ORF8', 'left': 'R', 'pos': 52, 'right': 'I'},
{'gene': 'ORF8', 'left': 'Y', 'pos': 73, 'right': 'C'}
],
"synonymous": [
{"left": "C", "pos": 241, "right": "T"},
{"left": "C", "pos": 913, "right": "T"},
{"left": "C", "pos": 3037, "right": "T"},
{"left": "C", "pos": 5986, "right": "T"},
{"left": "C", "pos": 14676, "right": "T"},
{"left": "C", "pos": 15279, "right": "T"},
{"left": "T", "pos": 16176, "right": "C"}
]
]
}

],

"mutations": {
"build_name": "S.E484",
"display_name": "S:E484",
// no pango name
"nextstrain_url": "https://nextstrain.org/groups/neherlab/ncov/S.E484?c=gt-S_484",
"covariants_url": "https://covariants.org/variants/S.E484",
"color": "#006600",
"defining_mutations": [
{
"type": "alignment_defining",
"mutations": [
// there is no 'to' base because currently the builds look for any change away from reference
"G23012" // S E484
]
},
{
"type": "phylogenetic_defining",
// this is same as alignment_defining for mutations
"mutations": [
"G23012"
]
}
]
}
}