Genotype Viewer

The Genotype Viewer interface queries the SNP genotype matrix constrained by genomic region and genotype dataset. The region is defined by the reference assembly, chromosome/contig, start and end or by selecting the gene locus. The interface uses the SNP-Seek software and database infrastructure developed by (Mansueto 2017) for the International Rice Informatics Consortium.

SNPs were generated using the raw reads from genome sequencing projects (CBDRx,Purple Kush, Finola, Jamaican Lion-DASH, and JL), WGS resequencing (Lynch 2016, McKernan 2020, Welling 2020), Kannapedia and Phylos FASTQs, called against CBDRx cs10 and Purple Kush pkv5 reference, and using the Parabricks germline pipeline. RNA-Seq samples were analyzed using the GATK RNAseq short variant discovery pipeline.SnpEff was then used on the variants and gene models (NCBI RefSeq for cs10, GeneMark-EP prediction for pkv5) to identify synonymous and non-synonymous SNPs. Indels will be available soon.

To query, select the reference (cs10, pkv5), cultivar and SNPs set, and the genomic region by specifying contig and range (limit to less than 500kb, but ideal for <10kb range). The chromosome and gene locus lists are auto-complete comboboxes. The lookup table for chromosome name to NCBI sequence accession ID is available here..

Genotype data sources and licences

Dataset

Source

6_wgs - 6 whole genome NGS datasets

Reference	Cultivars	Licence
Lynch 2016 10.1080/07352689.2016.1265363 PRJNA310948	(55) Afghan_Kush_1, Afghan_Kush_2, Afghan_Kush_3, Afghan_Kush_4, Afghan_Kush_5, Afghan_Kush_6, Alaskan_Thunderfuck, Auto_AK47, B-5, Blue_Dream_3, Blueberry_DJ, Cannatonic, Carmagnola_1, Carmagnola_2, Carmagnola_3, Carmagnola_4, Carmagnola_5, Carmagnola_6, Chem91, Chinese_hemp, Chocolope_1, Dagestani_hemp, Durban_Poison_1, Durban_Poison_2, EuroOil_2, Feral_Kansas, Feral_Nebraska_1, Feral_Nebraska_3, G13, Girl_Scout_Cookies_1, Golden_Goat_2, Grape_Ape_1, Harlequin, Hawaiian, Hindu_Kush, Jack_Herer_1, Kompolti_1, Kompolti_2, Kunduz, Lebanese, Liberty_Haze, Low_Ryder, Maui_Waui, OG_Kush, Original_Sour_Diesel, Pre-98_Bubba_Kush, R4, Rocky_Mountain_Bluberry, Sievers_Infinity, Skunk_#1, Somali_Taxi_Cab, Super_Lemon_Haze, Tangerine_Haze, Tora_Bora, White_Widow_1	NCBI data usage policy
McKernan 2020 10.1101/2020.01.03.894428 PRJNA575581	(40) 80 E-1, 80 E-2, 80 E-3, Arcata Trainwreck, Black 84, Black Beauty, BlueBerry Cheesecake X JL Male, C3/USO-1_F1_15_CSU, Carmagnola_3, Carmaleonte, Chem 91, Citrix, CS_1_2016_CSU, Domnesia, Eletta Campana, Fedora17_6_1_CSU, Grape Stomper, Harlox, Headcheese, Herijuana, IdaliaFT_1_CSU, Jamaican Lion ^4 #1, Jamaican Lion ^4 #2, Jamaican Lion ^4 #3, Jamaican Lion ^4 #4, Jamaican Lion ^4 #5, Jamaican Lion ^4 #6, Jamaican Lion^3 Father, Jamaican Lion^3 Mother, Jamaican Lion^3 Mother PCR, Master Kush, Merino_S_1_CSU, Mothers Milk #5, Red Eye OG, Saint Jack, Sour Diesel, Sour Tsunami, Sour Tsunami x Cataract Kush, Tahoe OG, Tiborszallasi	NCBI data usage policy
Kannapedia FASTQ	(58) AK47, AfghanKush, Afgooey, AlaskanIce, ArcataTrainWreck, ArjanUltraHaze2, AustralianBastard, BlueBerryCheeseCake18, BlueBerryCheeseCakeBC2Fem, BlueBerryEssense, BlueDreamSCC, Breakthrough, C4XCanatsuSCC, CBDMangoHaze, CanaTsuSCC, CaseyJones, CheeseGHS, ChemDawg91, ChemDawg, ChemDog18cycles, ChemDog, ChemdogXCherryPieSCC, Cinex, DakiniKushMale, DeepPurpleHaze, DiamondGirl, EastCoastSourDiesel, FireOG, G4XSFMSCC, GirlScoutCookie, GrapeStomper, GreenCrackSCC, Haleys, JackHerer, JambaCity, KushITSCC, LuckyCharms, MicheNepalMale, MoonshineHaze2, OGKushSCC, OGKushTest1, OGXPKSCC, PKX808OGSCC, PureKush, RedDevil, Ringo, RioNegraMale, RollexKush, SSHXWWSCC, SecretOG, SensiStarXSFMSCC, SnoopDream, SourTsunami, SuperLemonHaze, TrainwreckSCC, WIFIGTUBE, WIFI, WZ, Watermelonhazemale, WhiteWidow, WonderWoman, YeddiMale	No licence statement
Ren 2021 10.1126/sciadv.abg2286 PRJNA734114	(82) Uniko B HUO, Fibranova IFA, Kompolti HKI, Beniko PBO, Carmagnola 2 ICA2, Tiborszallasi HTI, Big Bud BBD, Big Skunk BSK, Delta-llosa SDA, Swaziland SWD, Ruderalis Indica RIA, Top 44 TOP, Northern Light NLT, Alpine Rocket ART, Haze HAE, Mexican Sativa MSA, Hawaii Maui Waui HMW, PP9, Hindu Kush HKH, Juso14 UJO, IUP1, IUP2, IUP3, B52, IUL1, IUL2, IUL3, IBR1, IBR2, IBR3, PID1, PID2, PCL1, PCL2, Bialobrzeskie PBE, VIR 469-1 KAK1, VIR 469-3 KAK3, VIR 469-2 KAK2, VIR 483-1 UTT1, VIR 483-2 UTT2, VIR 483-3 UTT3, R2in135-1 NER1, R1in136-1 ERM1, R3in134-1 NEB1, VIR 37, Novgorod-Seversky, cv UNS, Ferimon 12 FFN, VIR 201 UKE, VIR 369 BUA, VIR 493, Glukhovskaja 10 Zheltostebel'naja UGA, VIR 507, Krasnodarsky 10 FB RKY, IBE, R1in136-2 ERM2, R1in136-3 ERM3, R2in135-2 NER2, R2in135-3 NER3, R1in136-4 ERM4, Fedora 17 FFA, R3in134-2 NEB2, R2in135-4 NER4, R3in134-3 NEB3, VIR 223, Bernburgskaya Odnodomnaya, bm GBA, R3in134-4 NEB4, Wild Thailand THD, missing PEU, Colombian 8 COA, VIR 449, Szegedi 9 HIS, XHC1, Santhica 27 FSA, XHC2, XGL1, XGL2, XBL1, XBL2, XUM1, IMA, XUM2, SCN, QHI, Carmagnola 1 ICA1, YNN, GXI, Chamaeleon NCN	NCBI data usage policy
From various NGS sequencing projects	Welling 2020 10.1038/s41598-020-75271-7 PRJNA669610 (2) CBDA pool, THCVA pool Woods 2021 10.1093/genetics/iyab099 PRJNA723060 (3) Carmagnola, USO31, Carmagnola x USO31 F1	NCBI data usage policy
From genome assembly projects	CBDRx,Purple Kush, Finola, Jamaican Lion-DASH, and JL	NCBI data usage policy

7_wgs - update for 6_wgs

Reference

Cultivars

Licence

Woods 2022 PRJNA866500

10.1093/g3journal/jkac209

(135, w/ replicates) Bialobrzesk ,Carmagnola ,Carmealon ,Dac ,Dia ,Eletta Campa ,Fedora_17 ,Felina ,Ferimo ,Futura ,IPK_100 ,IPK_16 ,IPK_17 ,IPK_18 ,IPK_19 ,IPK_20 ,IPK_21 ,IPK_22 ,IPK_23 ,IPK_24 ,IPK_26 ,IPK_27 ,IPK_28 ,IPK_29 ,IPK_30 ,IPK_31 ,IPK_32 ,IPK_33 ,IPK_34 ,IPK_35 ,IPK_36 ,IPK_37 ,IPK_38 ,IPK_39 ,IPK_40 ,IPK_41 ,IPK_42 ,IPK_43 ,IPK_44 ,IPK_45 ,IPK_46 ,IPK_48 ,IPK_49 ,IPK_50 ,IPK_51 ,IPK_52 ,IPK_53 ,IPK_54 ,IPK_55 ,IPK_56 ,IPK_57 ,IPK_58 ,IPK_59 ,IPK_60 ,IPK_61 ,IPK_63 ,IPK_64 ,IPK_65 ,IPK_68 ,IPK_69 ,IPK_70 ,Jiang ,Lovr ,Meng ,Monoi ,Santhica_ ,Tiborszalla ,Tis ,Tyg ,US_feral ,USO_31

NCBI data usage policy

7_wgs_ nokann

7_wgs excluding the Kannapedia samples which have very low coverage than the rest

woods2022_cs10

From Woods 2022 doi.org/10.1093/g3journal/jkac209 vcf file https://doi.org/10.5061/dryad.rv15dv49q

wgs7ds_ gatk43

7_wgs but using newer GATK v4.3 GenomicsDB for combining gvcf files for joint genotyping. The other sets used GATK v4.1.7 GenomicsDB. v4.3 changed the allele representation of missing from dot to 0, resuting into most missing become reference allele, described in this blog.

phylos

2223 cultivars from Phylos collection. NCBI BioProjects PRJNA347566 PRJNA510566

NCBI data usage policy

trichome_rnaseq

Reference	Cultivars	Licence
Zager 2019 PRJNA498707	Sour Diesel, Canna Tsu, Black Lime, Valley Fire, White Cookies, Mama Thai, Terple, Cherry Chem, Blackberry Kush	NCBI data usage policy
Booth 2020 PRJNA599437	Afghan Kush,Blue Cheese,CBD Skunk Haze,Chocolope, Lemon Skunk	NCBI data usage policy
Livingston 2020 PRJNA483805	Finola bulbous, sesille,stalked	NCBI data usage policy
Braich 2019 SRR10600904,SRR10600906,SRR10600907 SRR10600908,SRR10600912,SRR10600913 SRR10600916,SRR10600918,SRR10600920 SRR10600922,SRR10600923,SRR10600925	Cannbio-2 trichome, 4 develoopment stages, 3 replicates	NCBI data usage policy

trichome26_rnaseq - update for trichome_rnaseq

Reference	Cultivars	Licence
Yeo 2022 PRJNA706039	chemdawg, headband, ghost_ogxbk, tahoe_ogxbk,westside	NCBI data usage policy