Date Range
Use this slider to filter the data based on the sample date. This may include inferred dates for ancestral nodes in the tree, and thus the date range here can be wider than the sample collection range.
2019-12-13
2023-03-25
Color By
Change the metadata field which the visualisation is coloured by.
The phylogeny, map and frequencies panel (if available) will all be coloured in a consistent fashion.
Country
Filter Data
Use this box to filter the displayed data based upon filtering criteria. For instance, start typing a country's name to filter the data accordingly.
Data is filtered by forming a union of selected values within each category, and then taking the intersection between categories (if more than one category is selected).
Scroll to the bottom of the main page (under the data visualisation) to see an expanded display of filters and available values.
Filter options prefixed with "(M)" are filters specific to the Measurements panel. They will have no effect on the phylogeny tree or other panels.
Type filter query here...
Tree
This panel displays the evolutionary relationships among samples, illustrating their genetic relatedness and inferred ancestry.
The exact options available depend on the dataset and specific analysis performed.
If Branch Length is available, you can choose to display the tree branches in terms of (nucleotide) divergence or (inferred) time. It is often helpful to toggle on confidence intervals to gauge the uncertainty in the reconstruction of internal node dates.
Layout
Branch Length
Branch Labels
clade
Tip Labels
Sample Name
Explode Tree By
Exploding a tree by trait X means that for each branch where the trait changes value, we will prune off the branch and create a separate (sub)tree. It works best when the trait doesn't change value too frequently.
Select...
Map
This panel displays the geographical distribution of samples.
The geographic resolution chooses the metadata values which define where samples are placed on the map. This can be the same as the selected color-by but is often not!
Geographic resolution
division
Entropy
This panel displays the observed diversity across the current genome or a selected CDS. All options are in the panel itself.
Frequency
This panel displays the prevalence of a characteristic over time, determined by the color-by.
Normalize frequencies controls whether the vertical axis represents the entire dataset or only the samples currently visible (e.g. due to filtering). This option is not available when data is limited to prevent numerical issues.
(Frequencies cannot be normalized)
Animation Options
Change various options relating to how the animation proceeds.
Animation Speed

Display
Control whether to show the tree and the map side-by-side (grid) or expanded (full).
Language
English
Phylogenetic analysis of SARS-CoV-2 diversity in Japan
Built with . Maintained by . Data updated 2023-03-30. Enabled by data from .
Showing 8530 of 8530 genomes sampled between Dec 2019 and Mar 2023.
Phylogeny
JapanJapanJapanQuarantineJapanQuarantineChinaChinaMalaysiaMalaysiaUSAUSAUnited KingdomUnited KingdomSouth KoreaSouth KoreaEquatorial GuineaEquatorial GuineaKazakhstanKazakhstanPanamaPanamaNicaraguaNicaraguaHondurasHondurasCôte d'IvoireCôte d'IvoireNew ZealandNew ZealandBurkina FasoBurkina FasoFijiFijiSomaliaSomaliaSudanSudanUgandaUgandaDemocratic Republic of the CongoDemocratic Republic of the CongoRwandaRwandaHong KongHong KongSierra LeoneSierra LeoneNigerNigerGuinea-BissauGuinea-BissauTogoTogoCanadaCanadaThailandThailandSingaporeSingaporeCambodiaCambodiaLithuaniaLithuaniaCuracaoCuracaoSouth AfricaSouth AfricaIndonesiaIndonesiaPapua New GuineaPapua New GuineaPhilippinesPhilippinesIcelandIcelandItalyItalyTimor-LesteTimor-LesteGermanyGermanyCameroonCameroonLibyaLibyaBeninBeninMauritaniaMauritaniaHungaryHungaryBermudaBermudaTunisiaTunisiaCyprusCyprusMadagascarMadagascarNepalNepalSaudi ArabiaSaudi ArabiaBosnia and HerzegovinaBosnia and HerzegovinaDenmarkDenmarkLebanonLebanonBhutanBhutanIranIranIraqIraqFinlandFinlandBangladeshBangladeshMyanmarMyanmarBahrainBahrainDominican RepublicDominican RepublicArgentinaArgentinaEgyptEgyptSwedenSwedenTurkeyTurkeyHaitiHaitiGhanaGhanaJordanJordanCentral African RepublicCentral African RepublicBelgiumBelgiumIndiaIndiaBelarusBelarusLatviaLatviaSerbiaSerbiaColombiaColombiaVenezuelaVenezuelaTrinidad and TobagoTrinidad and TobagoArubaArubaCabo VerdeCabo VerdeGuineaGuineaGabonGabonEthiopiaEthiopiaIrelandIrelandMaltaMaltaSenegalSenegalAlgeriaAlgeriaSri LankaSri LankaAustraliaAustraliaGeorgiaGeorgiaKenyaKenyaMozambiqueMozambiqueSaint Vincent and the GrenadinesSaint Vincent and the GrenadinesGrenadaGrenadaQatarQatarZimbabweZimbabweBotswanaBotswanaAngolaAngolaNamibiaNamibiaAntigua and BarbudaAntigua and BarbudaMalawiMalawiUnited Arab EmiratesUnited Arab EmiratesTanzaniaTanzaniaFranceFranceZambiaZambiaKuwaitKuwaitCosta RicaCosta RicaEswatiniEswatiniSeychellesSeychellesMonacoMonacoDjiboutiDjiboutiLiberiaLiberiaBurundiBurundiOmanOmanSouth SudanSouth SudanUzbekistanUzbekistanEl SalvadorEl SalvadorTaiwanTaiwanPolandPolandMoroccoMoroccoNorwayNorwayRomaniaRomaniaRepublic of the CongoRepublic of the CongoAustriaAustriaLaosLaosMongoliaMongoliaAlbaniaAlbaniaGuyanaGuyanaMaldivesMaldivesNetherlandsNetherlandsGreeceGreeceBahamasBahamasBelizeBelizeVietnamVietnamMauritiusMauritiusSolomon IslandsSolomon IslandsBruneiBruneiUkraineUkrainePalestinePalestineSint MaartenSint MaartenSaint BarthélemySaint BarthélemySpainSpainSao Tome and PrincipeSao Tome and PrincipeSloveniaSloveniaNigeriaNigeriaAzerbaijanAzerbaijanParaguayParaguayPalauPalauFrench PolynesiaFrench PolynesiaNorth MacedoniaNorth MacedoniaPortugalPortugalMexicoMexicoLuxembourgLuxembourgAndorraAndorraLiechtensteinLiechtensteinSwitzerlandSwitzerlandSaint LuciaSaint LuciaSyriaSyriaEstoniaEstoniaMontenegroMontenegroPeruPeruBulgariaBulgariaChadChadRussiaRussiaSlovakiaSlovakiaCroatiaCroatiaChileChileIsraelIsraelKyrgyzstanKyrgyzstanKosovoKosovoCzech RepublicCzech RepublicUruguayUruguayArmeniaArmeniaSurinameSurinameBoliviaBoliviaGuatemalaGuatemalaGambiaGambiaCubaCubaPakistanPakistanMoldovaMoldovaDominicaDominicaGuadeloupeGuadeloupeBarbadosBarbadosJamaicaJamaicaEcuadorEcuadorBrazilBrazilLesothoLesothoSaint Kitts and NevisSaint Kitts and NevisKiribatiKiribatiVanuatuVanuatuMarshall IslandsMarshall IslandsSaint MartinSaint MartinBonaireBonaireMicronesiaMicronesiaPuerto RicoPuerto RicoCountry2019-Dec2020-May2020-Oct2021-Mar2021-Aug2022-Jan2022-Jun2022-Nov2023-AprDate19A20A21A (Delta)20B21L (Omicron)22D (Omicron)22F (Omicron)23A (Omicron)22B (Omicron)22E (Omicron)
Geography
JapanJapanJapanQuarantineJapanQuarantineChinaChinaMalaysiaMalaysiaUSAUSAUnited KingdomUnited KingdomSouth KoreaSouth KoreaEquatorial GuineaEquatorial GuineaKazakhstanKazakhstanPanamaPanamaNicaraguaNicaraguaHondurasHondurasCôte d'IvoireCôte d'IvoireNew ZealandNew ZealandBurkina FasoBurkina FasoFijiFijiSomaliaSomaliaSudanSudanUgandaUgandaDemocratic Republic of the CongoDemocratic Republic of the CongoRwandaRwandaHong KongHong KongSierra LeoneSierra LeoneNigerNigerGuinea-BissauGuinea-BissauTogoTogoCanadaCanadaThailandThailandSingaporeSingaporeCambodiaCambodiaLithuaniaLithuaniaCuracaoCuracaoSouth AfricaSouth AfricaIndonesiaIndonesiaPapua New GuineaPapua New GuineaPhilippinesPhilippinesIcelandIcelandItalyItalyTimor-LesteTimor-LesteGermanyGermanyCameroonCameroonLibyaLibyaBeninBeninMauritaniaMauritaniaHungaryHungaryBermudaBermudaTunisiaTunisiaCyprusCyprusMadagascarMadagascarNepalNepalSaudi ArabiaSaudi ArabiaBosnia and HerzegovinaBosnia and HerzegovinaDenmarkDenmarkLebanonLebanonBhutanBhutanIranIranIraqIraqFinlandFinlandBangladeshBangladeshMyanmarMyanmarBahrainBahrainDominican RepublicDominican RepublicArgentinaArgentinaEgyptEgyptSwedenSwedenTurkeyTurkeyHaitiHaitiGhanaGhanaJordanJordanCentral African RepublicCentral African RepublicBelgiumBelgiumIndiaIndiaBelarusBelarusLatviaLatviaSerbiaSerbiaColombiaColombiaVenezuelaVenezuelaTrinidad and TobagoTrinidad and TobagoArubaArubaCabo VerdeCabo VerdeGuineaGuineaGabonGabonEthiopiaEthiopiaIrelandIrelandMaltaMaltaSenegalSenegalAlgeriaAlgeriaSri LankaSri LankaAustraliaAustraliaGeorgiaGeorgiaKenyaKenyaMozambiqueMozambiqueSaint Vincent and the GrenadinesSaint Vincent and the GrenadinesGrenadaGrenadaQatarQatarZimbabweZimbabweBotswanaBotswanaAngolaAngolaNamibiaNamibiaAntigua and BarbudaAntigua and BarbudaMalawiMalawiUnited Arab EmiratesUnited Arab EmiratesTanzaniaTanzaniaFranceFranceZambiaZambiaKuwaitKuwaitCosta RicaCosta RicaEswatiniEswatiniSeychellesSeychellesMonacoMonacoDjiboutiDjiboutiLiberiaLiberiaBurundiBurundiOmanOmanSouth SudanSouth SudanUzbekistanUzbekistanEl SalvadorEl SalvadorTaiwanTaiwanPolandPolandMoroccoMoroccoNorwayNorwayRomaniaRomaniaRepublic of the CongoRepublic of the CongoAustriaAustriaLaosLaosMongoliaMongoliaAlbaniaAlbaniaGuyanaGuyanaMaldivesMaldivesNetherlandsNetherlandsGreeceGreeceBahamasBahamasBelizeBelizeVietnamVietnamMauritiusMauritiusSolomon IslandsSolomon IslandsBruneiBruneiUkraineUkrainePalestinePalestineSint MaartenSint MaartenSaint BarthélemySaint BarthélemySpainSpainSao Tome and PrincipeSao Tome and PrincipeSloveniaSloveniaNigeriaNigeriaAzerbaijanAzerbaijanParaguayParaguayPalauPalauFrench PolynesiaFrench PolynesiaNorth MacedoniaNorth MacedoniaPortugalPortugalMexicoMexicoLuxembourgLuxembourgAndorraAndorraLiechtensteinLiechtensteinSwitzerlandSwitzerlandSaint LuciaSaint LuciaSyriaSyriaEstoniaEstoniaMontenegroMontenegroPeruPeruBulgariaBulgariaChadChadRussiaRussiaSlovakiaSlovakiaCroatiaCroatiaChileChileIsraelIsraelKyrgyzstanKyrgyzstanKosovoKosovoCzech RepublicCzech RepublicUruguayUruguayArmeniaArmeniaSurinameSurinameBoliviaBoliviaGuatemalaGuatemalaGambiaGambiaCubaCubaPakistanPakistanMoldovaMoldovaDominicaDominicaGuadeloupeGuadeloupeBarbadosBarbadosJamaicaJamaicaEcuadorEcuadorBrazilBrazilLesothoLesothoSaint Kitts and NevisSaint Kitts and NevisKiribatiKiribatiVanuatuVanuatuMarshall IslandsMarshall IslandsSaint MartinSaint MartinBonaireBonaireMicronesiaMicronesiaPuerto RicoPuerto RicoCountry
Data updated 2023-03-30Auspice v2.63.1
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