Garlic

RSP 11341

Grower: Happy Valley

Summary

Garlic (RSP11341/Happy Valley) is a genetic Type I plant and its genetics appear uncommon. The sample's closest relative in the database is Skywalker OG (RSP10837/THC Design) and it is a potential sibling. The heterozygosity rate is 1.2% which is higher than average (68.5 percentile).

General Information

Accession Date
October 17, 2019
Reported Plant Sex
Female

The strain rarity visualization shows how distant the strain is from the other cultivars in the Kannapedia database. The y-axis represents genetic distance, getting farther as you go up. The width of the visualization at any position along the y-axis shows how many strains there are in the database at that genetic distance. So, a common strain will have a more bottom-heavy shape, while uncommon and rare cultivars will have a visualization that is generally shifted towards the top.

Rarity: Uncommon
Most Distant Most Similar

Chemical Information

Cannabinoid and terpenoid information provided by the grower.

Cannabinoids

No information provided.

Terpenoids

No information provided.

Genetic Information

Plant Type
Type I

The bell curve in the heterozygosity visualization shows the distribution of heterozygosity levels for cannabis cultivars in the Kannapedia database. The green line shows where this particular strain fits within the distribution. Heterozygosity is associated with heterosis (aka hybrid vigor) but also leads to the production of more variable offspring. When plants have two genetically different parents, heterozygosity levels will be higher than if it has been inbred or backcrossed repeatedly.

Heterozygosity: 1.2%
Least Heterozygous Most Heterozygous

The ratio of reads mapped to Y-contigs to reads mapped to the whole Cannabis genome (Y-ratios) has been demonstrated to be strongly correlated with plant sex typing. This plot shows the distribution of Y-ratios for all samples in our database which were sequenced with the same method (panel or WGS) as this sample and where this sample falls in the distribution.

Y-Ratio Distribution: 0.0501
male female RSP11341

This chart represents the Illumina sequence coverage over the Bt/Bd allele. These are the three regions in the cannabis genome that impact THCA, CBDA, CBGA production. Coverage over the Active CBDAS gene is highly correlated with Type II and Type III plants as described by Etienne de Meijer. Coverage over the THCA gene is highly correlated with Type I and Type II plants but is anti-correlated with Type III plants. Type I plants require coverage over the inactive CBDA loci and no coverage over the Active CBDA gene. Lack of coverage over the Active CBDA and Active THCA allele are presumed to be Type IV plants (CBGA dominant). While deletions of entire THCAS and CBDAS genes are the most common Bt:Bd alleles observed, it is possible to have plants with these genes where functional expression of the enzyme is disrupted by deactivating point mutations (Kojoma et al. 2006).

Bt/Bd Allele Coverage

This chart represents the Illumina sequence coverage over the CBCA synthase gene.

CBCAS Coverage

Variants (THCAS, CBDAS, and CBCAS)

Gene HGVS.c HGVS.p Annotation Annotation Impact Contig Contig Pos Ref/Alt Var Freq
THCAS c.749C>A p.Ala250Asp missense variant moderate contig741 4417079

IGV: Start, Jump

G/T
NGS:
0.127
C90:
0.632

Variants (Select Genes of Interest)

PKSG-4a

UniProt

c.617A>G p.Tyr206Cys missense variant moderate contig700 1938028

IGV: Start, Jump

A/G
NGS:
0.075
C90:
0.000
PKSG-4a

UniProt

c.626_628delATA p.Asn209del disruptive inframe deletion moderate contig700 1938032

IGV: Start, Jump

CAAT/C
NGS:
0.075
C90:
0.000
PKSG-4a

UniProt

c.1191_1193delTTA p.Tyr398del disruptive inframe deletion moderate contig700 1938600

IGV: Start, Jump

AATT/A
NGS:
0.167
C90:
0.000
PKSG-2a

UniProt

c.1136G>A p.Arg379His missense variant moderate contig700 1944254

IGV: Start, Jump

C/T
NGS:
0.020
C90:
0.000
PKSG-2a

UniProt

c.948T>G p.Asp316Glu missense variant moderate contig700 1944442

IGV: Start, Jump

A/C
NGS:
0.079
C90:
0.000
PKSG-2a

UniProt

c.945T>G p.Ser315Arg missense variant moderate contig700 1944445

IGV: Start, Jump

A/C
NGS:
0.079
C90:
0.000
PKSG-2a

UniProt

c.944G>A p.Ser315Asn missense variant moderate contig700 1944446

IGV: Start, Jump

C/T
NGS:
0.079
C90:
0.000
PKSG-2a

UniProt

c.934C>G p.His312Asp missense variant moderate contig700 1944456

IGV: Start, Jump

G/C
NGS:
0.070
C90:
0.000
PKSG-2a

UniProt

c.67T>A p.Phe23Ile missense variant moderate contig700 1945567

IGV: Start, Jump

A/T
NGS:
0.825
C90:
0.904
PKSG-2a

UniProt

c.31A>T p.Thr11Ser missense variant moderate contig700 1945603

IGV: Start, Jump

T/A
NGS:
0.763
C90:
0.876
PKSG-2b

UniProt

c.1152T>A p.Asn384Lys missense variant moderate contig700 1950486

IGV: Start, Jump

A/T
NGS:
0.715
C90:
0.895
PKSG-2b

UniProt

c.1132C>G p.Leu378Val missense variant moderate contig700 1950506

IGV: Start, Jump

G/C
NGS:
0.717
C90:
0.000
PKSG-2b

UniProt

c.1124G>C p.Arg375Thr missense variant moderate contig700 1950514

IGV: Start, Jump

C/G
NGS:
0.015
C90:
0.000
PKSG-2b

UniProt

c.1117A>G p.Ile373Val missense variant moderate contig700 1950521

IGV: Start, Jump

T/C
NGS:
0.807
C90:
0.981
PKSG-2b

UniProt

c.995C>T p.Ser332Phe missense variant moderate contig700 1950643

IGV: Start, Jump

G/A
NGS:
0.042
C90:
0.000
PKSG-2b

UniProt

c.67A>T p.Ile23Phe missense variant moderate contig700 1951815

IGV: Start, Jump

T/A
NGS:
0.033
C90:
0.325
PKSG-2b

UniProt

c.31A>T p.Thr11Ser missense variant moderate contig700 1951851

IGV: Start, Jump

T/A
NGS:
0.844
C90:
0.880
PKSG-4b

UniProt

c.535_545delATTGGAGTGGG p.Ile179fs frameshift variant high contig700 2721127

IGV: Start, Jump

CCCCACTCCAAT/C
NGS:
0.105
C90:
0.000
PKSG-4b

UniProt

c.523C>T p.His175Tyr missense variant moderate contig700 2721150

IGV: Start, Jump

G/A
NGS:
0.112
C90:
0.325
PKSG-4b

UniProt

c.489delT p.Phe163fs frameshift variant high contig700 2721183

IGV: Start, Jump

CA/C
NGS:
0.792
C90:
0.761
PKSG-4b

UniProt

c.353_354insCC p.Gly119fs frameshift variant high contig700 2721319

IGV: Start, Jump

T/TGG
NGS:
0.175
C90:
0.000
DXR-2

UniProt

c.1319T>C p.Ile440Thr missense variant moderate contig380 285250

IGV: Start, Jump

A/G
NGS:
0.480
C90:
0.000
DXR-2

UniProt

c.431C>G p.Ala144Gly missense variant moderate contig380 287760

IGV: Start, Jump

G/C
NGS:
0.182
C90:
0.550
aPT4

UniProt

c.35A>C p.Gln12Pro missense variant moderate contig121 2828691

IGV: Start, Jump

A/C
NGS:
0.075
C90:
0.000
aPT1

UniProt

c.406A>G p.Ile136Val missense variant moderate contig121 2839605

IGV: Start, Jump

A/G
NGS:
0.579
C90:
0.761
HDS-2

UniProt

c.82_93delGTAACCGGAACT p.Val28_Thr31del conservative inframe deletion moderate contig95 1989748

IGV: Start, Jump

CGTAACCGGAACT/C
NGS:
0.805
C90:
0.000
HDS-2

UniProt

c.127T>G p.Ser43Ala missense variant moderate contig95 1989794

IGV: Start, Jump

T/G
NGS:
0.721
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.058 0.117 0.175 0.233
clone distance sibling distance more distant
  1. 0.166 Skywalker OG (RSP10837)
  2. 0.172 SFVxTK (RSP11072)
  3. 0.178 RKM-2018-013 (RSP11104)
  4. 0.178 RKM-2018-026 (RSP11118)
  5. 0.179 NSPM1 (RSP11362)
  6. 0.186 Red Eye OG (RSP11190)
  7. 0.191 Rugburn OG (RSP11353)
  8. 0.193 Star Dawg (RSP11352)
  9. 0.195 MENDO BREATH (RSP11242)
  10. 0.196 Hermaphrodite ResearchSample2 (RSP11050)
  11. 0.198 Gorilla Cookies (RSP11231)
  12. 0.203 Pie Hoe (RSP11073)
  13. 0.205 Abacus (RSP11266)
  14. 0.210 Sunday Driver (RSP11071)
  15. 0.214 RKM-2018-012 (RSP11103)
  16. 0.217 RKM-2018-034 (RSP11126)
  17. 0.218 Hermaphrodite ResearchSample2 (RSP11043)
  18. 0.222 Pure Power Plant (RSP11265)
  19. 0.222 501st OG (RSP11241)
  20. 0.224 The Gift (RSP10988)

Nearest genetic relatives (Base Tree)

0 0.075 0.150 0.225 0.300
clone distance sibling distance more distant
  1. 0.164 Skywalker OG (RSP10837)
  2. 0.179 RKM-2018-026 (RSP11118)
  3. 0.202 Hermaphrodite ResearchSample2 (RSP11050)
  4. 0.207 Pie Hoe (RSP11073)
  5. 0.213 RKM-2018-034 (RSP11126)
  6. 0.218 The Gift (RSP10988)
  7. 0.230 Sour Raspberry (RSP10551)
  8. 0.233 RKM-2018-005 (RSP11096)
  9. 0.240 RKM-2018-032 (RSP11124)
  10. 0.242 RKM-2018-002 (RSP11093)
  11. 0.242 RKM-2018-033 (RSP11125)
  12. 0.247 Blueberry Cheesecake (RSP10680)
  13. 0.249 Blueberry Cheesecake (RSP10684)
  14. 0.252 Kimbo Slice (RSP10997)
  15. 0.259 Hermaphrodite Research Sample1 (RSP11049)
  16. 0.263 RKM-2018-009 (RSP11100)
  17. 0.267 RKM-2018-020 (RSP11112)
  18. 0.268 Recon (RSP10755)
  19. 0.269 RKM-2018-029 (RSP11121)
  20. 0.271 RKM-2018-022 (RSP11114)

Most genetically distant strains (All Samples)

0 0.142 0.283 0.425 0.567
clone distance sibling distance more distant
  1. 0.536 Cherry Blossom (RSP11318)
  2. 0.502 Unknown- Cherry Wine - 001 (RSP11268)
  3. 0.498 Cherry Blossom (RSP11323)
  4. 0.489 Cherry Blossom (RSP11325)
  5. 0.475 Cherry Blossom (RSP11301)
  6. 0.473 Unknown- Cherry Wine - 002 (RSP11269)
  7. 0.469 Cherry Blossom (RSP11274)
  8. 0.467 Cherry Blossom (RSP11315)
  9. 0.466 Cherry Blossom (RSP11328)
  10. 0.464 Cherry Blossom (RSP11300)
  11. 0.459 Cherry Blossom (RSP11331)
  12. 0.455 Cherry Blossom (RSP11306)
  13. 0.454 Wife (RSP11148)
  14. 0.450 Cherry Blossom (RSP11310)
  15. 0.450 Cherry Blossom (RSP11312)
  16. 0.449 Cherry Blossom (RSP11319)
  17. 0.447 Cherry Blossom (RSP11302)
  18. 0.445 Unknown- Cherry Wine - 003 (RSP11270)
  19. 0.443 Cherry Blossom (RSP11311)
  20. 0.440 Cherry Blossom (RSP11334)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.378 Cbot-2019-005 (RSP11133)
  2. 0.373 Cherry (RSP11143)
  3. 0.370 Cbot-2019-001 (RSP11129)
  4. 0.363 JL yellow (RSP11075)
  5. 0.363 Cbot-2019-004 (RSP11132)
  6. 0.344 Cherry (RSP11142)
  7. 0.343 Black Beauty (RSP11035)
  8. 0.342 RKM-2018-006 (RSP11097)
  9. 0.334 QUEEN JESUS (RSP10105)
  10. 0.330 RKM-2018-023 (RSP11115)
  11. 0.327 UP Sunrise (RSP10989)
  12. 0.324 Lovrin (RSP10658)
  13. 0.324 Blueberry Cheesecake (RSP10672)
  14. 0.321 RKM-2018-028 (RSP11120)
  15. 0.319 RKM-2018-018 (RSP11110)
  16. 0.319 Carmagnola (RSP11037)
  17. 0.317 RKM-2018-003 (RSP11094)
  18. 0.315 Futura 75 (RSP10664)
  19. 0.314 RKM-2018-019 (RSP11111)
  20. 0.313 Feral (RSP10890)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR8347212
Overlapping SNPs:
62
Concordance:
46

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495270
Overlapping SNPs:
6
Concordance:
6

Blockchain Registration Information

Transaction ID
124e50e295e023cbffad793da7c2b0d7a2dc6d2376029a75631913ad8e5ec443
Stamping Certificate
Download PDF (856.9 KB)
SHASUM Hash
75bbe91351a381becb259a78dfc6702d7d57c7cf15dd7354ae688e9ce120396d
QR code for RSP11341

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