Genotype Viewer

Creative Commons Licence

Help  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 2020Ren 2021Woods 2021), Kannapedia and Phylos FASTQs, called against CBDRx cs10Purple Kush pkv5 and Finola fnv2 reference 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 KushFinolaJamaican Lion-DASH, and JL NCBI data usage policy
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