cd2c57b40633f481b204fdd59b7e1ca212ecd04d angie Thu Mar 23 20:11:44 2023 -0700 Updating the very outdated Nextstrain Clade subtrack stanzas. diff --git src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra index 7275abb..3815b51 100644 --- src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra +++ src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra @@ -1,359 +1,759 @@ track nextstrainGene shortLabel Nextstrain Genes longLabel Genes annotated by nextstrain.org/ncov type bigBed 4 visibility hide group genes bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainGene.bb track nextstrainClade shortLabel Nextstrain Clades longLabel Nextstrain year-letter clade designations (19A, 19B, 20A, etc.) type bigBed 12 + itemRgb on visibility hide group varRep priority 0.5 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainClade.bb url https://nextstrain.org/ncov?d=tree&m=div&label=clade:$$ urlLabel View in Nextstrain: pennantIcon Updated red ../goldenPath/newsarch.html#071720 "Now updated daily" track nextstrainSamples shortLabel Nextstrain Mutations longLabel Nextstrain Subset of GISAID EpiCoV TM Sample Mutations type vcfTabix visibility hide hapClusterEnabled on hapClusterHeight 500 tableBrowser off vcfDoQual off vcfDoFilter off group varRep priority 0.51 hapClusterColorBy function geneTrack ncbiGeneBGP subGroup1 view Views all=All_Samples newClades=Year-Letter_Clades compositeTrack on pennantIcon Updated red ../goldenPath/newsarch.html#071720 "Now updated daily" track nextstrainSamplesViewAll view all parent nextstrainSamples shortLabel All Samples visibility squish track nextstrainSamplesRb parent nextstrainSamplesViewAll on subGroups view=all shortLabel Rec Bi-allelic longLabel Recurrent Bi-allelic Mutations in Nextstrain Subset of GISAID EpiCoV TM Samples hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain.nh hapClusterHeight 500 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainRecurrentBiallelic.vcf.gz priority 1 track nextstrainSamplesAll parent nextstrainSamplesViewAll off subGroups view=all shortLabel All longLabel Mutations in Nextstrain Subset of GISAID EpiCov TM Samples hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain.nh hapClusterHeight 500 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples.vcf.gz priority 2 track nextstrainSamplesViewNewClades view newClades parent nextstrainSamples shortLabel Year-Letter Clades visibility hide track nextstrainSamples19A - parent nextstrainSamplesViewNewClades on + parent nextstrainSamplesViewNewClades subGroups view=newClades shortLabel 19A Mutations longLabel Mutations in Clade 19A Nextstrain Subset of GISAID EpiCoV TM Samples hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain19A.nh hapClusterHeight 300 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples19A.vcf.gz priority 10 track nextstrainSamples19B - parent nextstrainSamplesViewNewClades on + parent nextstrainSamplesViewNewClades subGroups view=newClades shortLabel 19B Mutations longLabel Mutations in Clade 19B Nextstrain Subset of GISAID EpiCoV TM Samples hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain19B.nh hapClusterHeight 300 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples19B.vcf.gz priority 20 track nextstrainSamples20A - parent nextstrainSamplesViewNewClades on + parent nextstrainSamplesViewNewClades subGroups view=newClades shortLabel 20A Mutations longLabel Mutations in Clade 20A Nextstrain Subset of GISAID EpiCoV TM Samples hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20A.nh hapClusterHeight 300 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20A.vcf.gz priority 30 track nextstrainSamples20B - parent nextstrainSamplesViewNewClades on + parent nextstrainSamplesViewNewClades subGroups view=newClades shortLabel 20B Mutations longLabel Mutations in Clade 20B Nextstrain Subset of GISAID EpiCoV TM Samples hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20B.nh hapClusterHeight 300 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20B.vcf.gz priority 40 track nextstrainSamples20C - parent nextstrainSamplesViewNewClades on + parent nextstrainSamplesViewNewClades subGroups view=newClades shortLabel 20C Mutations longLabel Mutations in Clade 20C Nextstrain Subset of GISAID EpiCoV TM Samples hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20C.nh hapClusterHeight 300 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20C.vcf.gz priority 50 track nextstrainSamples20D - parent nextstrainSamplesViewNewClades on + parent nextstrainSamplesViewNewClades subGroups view=newClades shortLabel 20D Mutations longLabel Mutations in Clade 20D Nextstrain Subset of GISAID EpiCoV TM Samples hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20D.nh hapClusterHeight 300 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20D.vcf.gz priority 50 track nextstrainSamples20E_EU1 - parent nextstrainSamplesViewNewClades on + parent nextstrainSamplesViewNewClades subGroups view=newClades shortLabel 20E/EU1 Mutations longLabel Mutations in Clade 20E/EU1 Nextstrain Subset of GISAID EpiCoV TM Samples hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20E_EU1.nh hapClusterHeight 300 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20E_EU1.vcf.gz priority 50 track nextstrainSamples20F - parent nextstrainSamplesViewNewClades on + parent nextstrainSamplesViewNewClades subGroups view=newClades shortLabel 20F Mutations longLabel Mutations in Clade 20F Nextstrain Subset of GISAID EpiCoV TM Samples hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20F.nh hapClusterHeight 300 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20F.vcf.gz priority 50 track nextstrainSamples20G - parent nextstrainSamplesViewNewClades on + parent nextstrainSamplesViewNewClades subGroups view=newClades shortLabel 20G Mutations longLabel Mutations in Clade 20G Nextstrain Subset of GISAID EpiCoV TM Samples hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20G.nh hapClusterHeight 300 bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20G.vcf.gz priority 50 - track nextstrainSamples20H_501Y_V2 + track nextstrainSamples20H_Beta + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 20H/Beta Mutations + longLabel Mutations in Clade 20H/501Y.V2/Beta Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20H_Beta_V2.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20H_Beta_V2.vcf.gz + priority 50 + + track nextstrainSamples20I_Alpha + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 20I/Alpha Mutations + longLabel Mutations in Clade 20I/501Y.V1/Alpha Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20I_Alpha_V1.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20I_Alpha_V1.vcf.gz + priority 50 + + track nextstrainSamples20J_Gamma + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 20J/Gamma Mutations + longLabel Mutations in Clade 20J/501Y.V3/Gamma Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20J_Gamma_V3.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20J_Gamma_V3.vcf.gz + priority 50 + + track nextstrainSamples21A_Delta + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 21A/Delta Mutations + longLabel Mutations in Clade 21A/Delta Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21A_Delta.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21A_Delta.vcf.gz + priority 50 + + track nextstrainSamples21B_Kappa parent nextstrainSamplesViewNewClades on subGroups view=newClades - shortLabel 20H/501Y.V2 Mutations - longLabel Mutations in Clade 20H/501Y.V2 Nextstrain Subset of GISAID EpiCoV TM Samples - hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20H_501Y.V2.nh + shortLabel 21B/Kappa Mutations + longLabel Mutations in Clade 21B/Kappa Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21B_Kappa.nh hapClusterHeight 300 - bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20H_501Y.V2.vcf.gz + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21B_Kappa.vcf.gz priority 50 - track nextstrainSamples20I_501Y_V1 + track nextstrainSamples21C_Epsilon parent nextstrainSamplesViewNewClades on subGroups view=newClades - shortLabel 20I/501Y.V1 Mutations - longLabel Mutations in Clade 20I/501Y.V1 Nextstrain Subset of GISAID EpiCoV TM Samples - hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20I_501Y.V1.nh + shortLabel 21C/Epsilon Mutations + longLabel Mutations in Clade 21C/Epsilon Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21C_Epsilon.nh hapClusterHeight 300 - bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20I_501Y.V1.vcf.gz + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21C_Epsilon.vcf.gz priority 50 - track nextstrainSamples20J_501Y_V3 + track nextstrainSamples21D_Eta parent nextstrainSamplesViewNewClades on subGroups view=newClades - shortLabel 20J/501Y.V3 Mutations - longLabel Mutations in Clade 20J/501Y.V3 Nextstrain Subset of GISAID EpiCoV TM Samples - hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain20J_501Y.V3.nh + shortLabel 21D/Eta Mutations + longLabel Mutations in Clade 21D/Eta Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21D_Eta.nh hapClusterHeight 300 - bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20J_501Y.V3.vcf.gz + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21D_Eta.vcf.gz + priority 50 + + track nextstrainSamples21E_Theta + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 21E/Theta Mutations + longLabel Mutations in Clade 21E/Theta Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21E_Theta.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21E_Theta.vcf.gz + priority 50 + + track nextstrainSamples21F_Iota + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 21F/Iota Mutations + longLabel Mutations in Clade 21F/Iota Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21F_Iota.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21F_Iota.vcf.gz + priority 50 + + track nextstrainSamples21G_Lambda + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 21G/Lambda Mutations + longLabel Mutations in Clade 21G/Lambda Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21G_Lambda.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21G_Lambda.vcf.gz + priority 50 + + track nextstrainSamples21H_Mu + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 21H/Mu Mutations + longLabel Mutations in Clade 21H/Mu Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21H_Mu.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21H_Mu.vcf.gz + priority 50 + + track nextstrainSamples21I_Delta + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 21I/Delta Mutations + longLabel Mutations in Clade 21I/Delta Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21I_Delta.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21I_Delta.vcf.gz + priority 50 + + track nextstrainSamples21J_Delta + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 21J/Delta Mutations + longLabel Mutations in Clade 21J/Delta Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21J_Delta.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21J_Delta.vcf.gz + priority 50 + + track nextstrainSamples21K_Omicron + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 21K/BA.1 Mutations + longLabel Mutations in Clade 21K/Omicron/BA.1 Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21K_Omicron.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21K_Omicron.vcf.gz + priority 50 + + track nextstrainSamples21L_Omicron + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 21L/BA.2 Mutations + longLabel Mutations in Clade 21L/Omicron/BA.2 Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21L_Omicron.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21L_Omicron.vcf.gz + priority 50 + + track nextstrainSamples21M_Omicron + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 21M/B.1.1.529 Mutations + longLabel Mutations in Clade 21M/Omicron/B.1.1.529 Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain21M_Omicron.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21M_Omicron.vcf.gz + priority 50 + + track nextstrainSamples22A_Omicron + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 22A/BA.4 Mutations + longLabel Mutations in Clade 22A/Omicron/BA.4 Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain22A_Omicron.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22A_Omicron.vcf.gz + priority 50 + + track nextstrainSamples22B_Omicron + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 22B/BA.5 Mutations + longLabel Mutations in Clade 22B/Omicron/BA.5 Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain22B_Omicron.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22B_Omicron.vcf.gz + priority 50 + + track nextstrainSamples22C_Omicron + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 22C/BA.2.12.1 Mutations + longLabel Mutations in Clade 22C/Omicron/BA.2.12.1 Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain22C_Omicron.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22C_Omicron.vcf.gz + priority 50 + + track nextstrainSamples22D_Omicron + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 22D/BA.2.75 Mutations + longLabel Mutations in Clade 22D/Omicron/BA.2.75 Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain22D_Omicron.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22D_Omicron.vcf.gz + priority 50 + + track nextstrainSamples22E_Omicron + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 22E/BQ.1 Mutations + longLabel Mutations in Clade 22E/Omicron/BQ.1 Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain22E_Omicron.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22E_Omicron.vcf.gz + priority 50 + + track nextstrainSamples22F_Omicron + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 22F/XBB Mutations + longLabel Mutations in Clade 22F/Omicron/XBB Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain22F_Omicron.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22F_Omicron.vcf.gz + priority 50 + + track nextstrainSamples23A_Omicron + parent nextstrainSamplesViewNewClades on + subGroups view=newClades + shortLabel 23A/XBB.1.5 Mutations + longLabel Mutations in Clade 23A/Omicron/XBB.1.5 Nextstrain Subset of GISAID EpiCoV TM Samples + hapClusterMethod treeFile /gbdb/wuhCor1/nextstrain/nextstrain23A_Omicron.nh + hapClusterHeight 300 + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples23A_Omicron.vcf.gz priority 50 track nextstrainFreq shortLabel Nextstrain Frequency longLabel Nextstrain Mutations Alternate Allele Frequency type bigWig compositeTrack on subGroup1 view Views all=All_Samples newClades=Year-Letter_Clades visibility hide group varRep autoScale off viewLimits 0:1.0 viewLimitsMax 0:1.0 maxHeightPixels 100:40:8 pennantIcon Updated red ../goldenPath/newsarch.html#071720 "Now updated daily" track nextstrainFreqViewAll view all parent nextstrainFreq shortLabel All Samples visibility pack track nextstrainFreqAll shortLabel All longLabel Nextstrain, all samples: Alternate allele frequency type bigWig bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples.bigWig visibility dense parent nextstrainFreqViewAll subGroups view=all priority 1 track nextstrainFreqViewNewClades view newClades parent nextstrainFreq shortLabel Year-Letter Clades visibility hide track nextstrainFreq19A shortLabel 19A longLabel Nextstrain, 19A clade: Alternate allele frequency type bigWig bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples19A.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 10 track nextstrainFreq19B shortLabel 19B longLabel Nextstrain, 19B clade: Alternate allele frequency type bigWig bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples19B.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 20 track nextstrainFreq20A shortLabel 20A longLabel Nextstrain, 20A clade: Alternate allele frequency type bigWig bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20A.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 30 track nextstrainFreq20B shortLabel 20B longLabel Nextstrain, 20B clade: Alternate allele frequency type bigWig bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20B.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 40 track nextstrainFreq20C shortLabel 20C longLabel Nextstrain, 20C clade: Alternate allele frequency type bigWig bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20C.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 50 track nextstrainFreq20D shortLabel 20D longLabel Nextstrain, 20D clade: Alternate allele frequency type bigWig bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20D.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 50 track nextstrainFreq20E_EU1 shortLabel 20E/EU1 longLabel Nextstrain, 20E_EU1 clade: Alternate allele frequency type bigWig bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20E_EU1.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 50 track nextstrainFreq20F shortLabel 20F longLabel Nextstrain, 20F clade: Alternate allele frequency type bigWig bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20F.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 50 track nextstrainFreq20G shortLabel 20G longLabel Nextstrain, 20G clade: Alternate allele frequency type bigWig bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20G.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 50 - track nextstrainFreq20H_501Y.V2 - shortLabel 20H/501Y.V2 - longLabel Nextstrain, 20H/501Y.V2 clade: Alternate allele frequency + track nextstrainFreq20H_Beta + shortLabel 20H/Beta + longLabel Nextstrain, 20H/501Y.V2/Beta clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20H_Beta_V2.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq20I_Alpha + shortLabel 20I/Alpha + longLabel Nextstrain, 20I/501Y.V1/Alpha clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20I_Alpha_V1.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq20J_Gamma + shortLabel 20J/Gamma + longLabel Nextstrain, 20J/501Y.V3/Gamma clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20J_Gamma_V3.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21A_Delta + shortLabel 21A/Delta + longLabel Nextstrain, 21A/Delta clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21A_Delta.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21B_Kappa + shortLabel 21B/Kappa + longLabel Nextstrain, 21B/Kappa clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21B_Kappa.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21C_Epsilon + shortLabel 21C/Epsilon + longLabel Nextstrain, 21C/Epsilon clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21C_Epsilon.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21D_Eta + shortLabel 21D/Eta + longLabel Nextstrain, 21D/Eta clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21D_Eta.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21E_Theta + shortLabel 21E/Theta + longLabel Nextstrain, 21E/Theta clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21E_Theta.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21F_Iota + shortLabel 21F/Iota + longLabel Nextstrain, 21F/Iota clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21F_Iota.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21G_Lambda + shortLabel 21G/Lambda + longLabel Nextstrain, 21G/Lambda clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21G_Lambda.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21H_Mu + shortLabel 21H/Mu + longLabel Nextstrain, 21H/Mu clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21H_Mu.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21I_Delta + shortLabel 21I/Delta + longLabel Nextstrain, 21I/Delta clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21I_Delta.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21J_Delta + shortLabel 21J/Delta + longLabel Nextstrain, 21J/Delta clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21J_Delta.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21K_Omicron + shortLabel 21K/BA.1 + longLabel Nextstrain, 21K/Omicron/BA.1 clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21K_Omicron.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21L_Omicron + shortLabel 21L/BA.2 + longLabel Nextstrain, 21L/Omicron/BA.2 clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21L_Omicron.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq21M_Omicron + shortLabel 21M/B.1.1.529 + longLabel Nextstrain, 21M/Omicron/B.1.1.529 clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples21M_Omicron.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq22A_Omicron + shortLabel 22A/BA.4 + longLabel Nextstrain, 22A/Omicron/BA.4 clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22A_Omicron.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq22B_Omicron + shortLabel 22B/BA.5 + longLabel Nextstrain, 22B/Omicron/BA.5 clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22B_Omicron.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq22C_Omicron + shortLabel 22C/BA.2.12.1 + longLabel Nextstrain, 22C/Omicron/BA.2.12.1 clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22C_Omicron.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq22D_Omicron + shortLabel 22D/BA.2.75 + longLabel Nextstrain, 22D/Omicron/BA.2.75 clade: Alternate allele frequency + type bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22D_Omicron.bigWig + visibility dense + parent nextstrainFreqViewNewClades + subGroups view=newClades + priority 50 + + track nextstrainFreq22E_Omicron + shortLabel 22E/BQ.1 + longLabel Nextstrain, 22E/Omicron/BQ.1 clade: Alternate allele frequency type bigWig - bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20H_501Y.V2.bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22E_Omicron.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 50 - track nextstrainFreq20J_501Y.V3 - shortLabel 20J/501Y.V3 - longLabel Nextstrain, 20J/501Y.V3 clade: Alternate allele frequency + track nextstrainFreq22F_Omicron + shortLabel 22F/XBB + longLabel Nextstrain, 22F/Omicron/XBB clade: Alternate allele frequency type bigWig - bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20J_501Y.V3.bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples22F_Omicron.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 50 - track nextstrainFreq20J_501Y_V3 - shortLabel 20J/501Y.V3 - longLabel Nextstrain, 20J/501Y.V3 clade: Alternate allele frequency + track nextstrainFreq23A_Omicron + shortLabel 23A/XBB.1.5 + longLabel Nextstrain, 23A/Omicron/XBB.1.5 clade: Alternate allele frequency type bigWig - bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples20J_501Y.V3.bigWig + bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainSamples23A_Omicron.bigWig visibility dense parent nextstrainFreqViewNewClades subGroups view=newClades priority 50 track nextstrainParsimony shortLabel Nextstrain Parsimony longLabel Parsimony Scores for Nextstrain Mutations and Phylogenetic Tree type bigWig bigDataUrl /gbdb/wuhCor1/nextstrain/nextstrainParsimony.bw group varRep visibility hide autoScale off viewLimits 0:60 maxHeightPixels 100:40:8 pennantIcon Updated red ../goldenPath/newsarch.html#071720 "Now updated daily"