JBrowse Genome Browser


HelpThe JBrowse genome browser allows you to visually explore genomes and their associated large-scale datasets. JBrowse is a widely used application that is fast, intuitive, and compatible with most web browsers. The lookup table for chromosome name to NCBI sequence accession ID is available here

Description and source of tracks

Genome assemblies and annotations

Genomic Variants

  • Phylos - SNPs generated by RevGenomics from the Phylos samples CC-BY-4.0
  • SCU reanalysis
    • SNPs, Indels SnpEff - variant effects to the genes using the SNPEff software, displayed using the varianteffect JBrowse plugin. The features are color coded with: Green - Synonymous, Purple - NonSynonymous, Red - Truncation/Stop gained, Blue - Intron/other.
    • SNPs Samples - SNPs for all samples in the dataset displayed using multivariantviewer JBrowse plugin. Color code: Gray - Reference Homozygous, Red - Alternative Homozygous, Yellow - Heterozygous, White - Missing
    • SNPs datasets were generated from raw read sequences described in detail in the Genotype Viewer page


  • Dataset

    Method Samples Datasource Reference
    canSat3 Aligned with cs10 and pkv5 assemblies using minimap2 in splice alignment mode Purple Kush canSat3_transcriptome-representative.fa.gz van Bakel 2011
    finola1 Finola finola1_transcriptome-representative.fa.gz van Bakel 2011
    Cannbio-2 Cannbio-2 GIFP01000001:GIFP01064413 Braich 2019
    5 transcripts

    1. Clustered (mmseq2 cm2 80% identity) transcript assemblies combined from  5  data sources

    2. Aligned to cs10 and pkv5 assemblies using minimap2 in splice alignment mode

    Purple Kush canSat3_transcriptome-full.fa.gz van Bakel 2011
    Finola finola1_transcriptome-full.fa.gz van Bakel 2011
    Cannbio-2 GIFP01000001:GIFP01064413 Braich 2019
    Terpene synthase genes from various C. sativa cultivars AB057805.1, AB164375.1, AB164375.1, AB292682.1, CcTHCAs, CsCBDAs, KY014554.1, KY014555.1, KY014556.1, KY014557.1, KY014558.2, KY014559.1, KY014560.1, KY014561.1, KY014562.1, KY014563.1, KY014564.1, KY014565.1, MK131289.1, MK131290.1, MK614217.1, MK801762.1, MK801763.1, MK801764.1, MK801765.1, MK801766.1, MN967470.1, MN967471.1, MN967472.1, MN967473.1, MN967474.1, MN967475.1, MN967477.1, MN967479.1, MN967480.1, MN967481.1, MN967481.1, MN967482.2, MN967483.1, MN967484.1, MnCBDAs-like, MT295505.1, MT295506.1, TPS11, TPS11-like, TPS12, TPS12-like, TPS13-like1, TPS13-like2, TPS14, TPS17, TPS20, TPS23, TPS24, TPS30-like, TPS32, TPS36, TPS37, TPS38, TPS40, TPS41, TPS42, TPS43, TPS44, TPS46, TPS47, TPS48, TPS49, TPS4-like, TPS50, TPS51, TPS52, TPS53, TPS55, TPS58, TPS59, TPS60, TPS61, TPS62, TPS63, TPS64, TPS6-like, TPS7_Finola, TPS8-like, TPS9, TPS9-like1, TPS9-like2

    Booth 2020Zager 2019 , Allen 2020

    Cannabinoid synthase genes from Argvana Heart  and Tachllta cultivars GHVF01000001-GHVF01000012,  GHVG01000001-GHVG01000012 McGarvey 2020

    21 trichomes samples

    (16 trichome excludes PRJNA599437)

    1. Fastq raw reads from trichome RNA-Seq experiments were assembled using rnaspades

    2.a  (BAM) Transcript assemblies were aligned to cs10 and pkv5 assemblies using minimap2 in splice alignment mode

    2.b (TMM) Transcript assembly expression levels are quantified using Salmon, and mapped to genome using TransDecoder

    2.Sour Diesel, Canna Tsu, Black Lime, Valley Fire, White Cookies, Mama Thai, Terple, Cherry Chem, Blackberry Kush PRJNA498707 Zager 2019
    Afghan Kush,Blue Cheese,CBD Skunk Haze,Chocolope, Lemon Skunk PRJNA599437 Booth 2020
    Finola bulbous, sesille,stalked PRJNA483805  Livingston 2020
    Cannbio-2 trichome, 4 develoopment stages SRR10600922, SRR10600916SRR10600908SRR10600906 Braich 2019