R4

RSP 11617

Grower: Plant Genomic Laboratory, Medicinal Plant Research Institute

General Information

Sample Name
CS Sativa
Accession Date
July 20, 2020
Reported Plant Sex
not reported

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: Rare
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 III

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: 1.36%
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: 0.1061
male female RSP11617

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
CBDAS c.353G>A p.Gly118Asp missense variant moderate contig1772 2082579

IGV: Start, Jump

G/A
NGS:
0.002
C90:
0.000

Variants (Select Genes of Interest)

GPPs1

UniProt

c.845_848delAAAG p.Glu282fs frameshift variant high contig676 169629

IGV: Start, Jump

TGAAA/T
NGS:
0.118
C90:
0.000
PKSG-2a

UniProt

c.774G>A p.Met258Ile missense variant moderate contig700 1944616

IGV: Start, Jump

C/T
NGS:
0.123
C90:
0.000
PKSG-2a

UniProt

c.241G>A p.Val81Met missense variant moderate contig700 1945149

IGV: Start, Jump

C/T
NGS:
0.136
C90:
0.000
PKSG-2a

UniProt

c.240T>G p.Asp80Glu missense variant moderate contig700 1945150

IGV: Start, Jump

A/C
NGS:
0.136
C90:
0.000
PKSG-2a

UniProt

c.230T>C p.Val77Ala missense variant moderate contig700 1945160

IGV: Start, Jump

A/G
NGS:
0.114
C90:
0.000
PKSG-2a

UniProt

c.224A>G p.Lys75Arg missense variant moderate contig700 1945166

IGV: Start, Jump

T/C
NGS:
0.143
C90:
0.962
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.1117A>G p.Ile373Val missense variant moderate contig700 1950521

IGV: Start, Jump

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

UniProt

c.774G>A p.Met258Ile missense variant moderate contig700 1950864

IGV: Start, Jump

C/T
NGS:
0.366
C90:
0.947
PKSG-2b

UniProt

c.241G>A p.Val81Met missense variant moderate contig700 1951397

IGV: Start, Jump

C/T
NGS:
0.154
C90:
0.000
PKSG-2b

UniProt

c.240T>G p.Asp80Glu missense variant moderate contig700 1951398

IGV: Start, Jump

A/C
NGS:
0.156
C90:
0.000
PKSG-2b

UniProt

c.230T>C p.Val77Ala missense variant moderate contig700 1951408

IGV: Start, Jump

A/G
NGS:
0.134
C90:
0.646
PKSG-2b

UniProt

c.224A>G p.Lys75Arg missense variant moderate contig700 1951414

IGV: Start, Jump

T/C
NGS:
0.151
C90:
0.957
PKSG-2b

UniProt

c.188T>G p.Ile63Ser missense variant moderate contig700 1951450

IGV: Start, Jump

A/C
NGS:
0.118
C90:
0.000
PKSG-2b

UniProt

c.187A>T p.Ile63Phe missense variant moderate contig700 1951451

IGV: Start, Jump

T/A
NGS:
0.116
C90:
0.000
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-2b

UniProt

c.-2_1dupATA start lost & conservative inframe insertion high contig700 1951880

IGV: Start, Jump

A/ATAT
NGS:
0.410
C90:
0.000
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.352_355delACAG p.Thr118fs frameshift variant high contig700 2721317

IGV: Start, Jump

CCTGT/C
NGS:
0.529
C90:
0.000
PKSG-4b

UniProt

c.324A>C p.Glu108Asp missense variant moderate contig700 2721349

IGV: Start, Jump

T/G
NGS:
0.094
C90:
0.000
PKSG-4b

UniProt

c.323A>G p.Glu108Gly missense variant moderate contig700 2721350

IGV: Start, Jump

T/C
NGS:
0.469
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
FAD2-2

UniProt

c.164A>G p.His55Arg missense variant moderate contig83 1803205

IGV: Start, Jump

T/C
NGS:
0.037
C90:
0.000
FAD2-2

UniProt

c.161T>A p.Leu54His missense variant moderate contig83 1803208

IGV: Start, Jump

A/T
NGS:
0.156
C90:
0.000
FAD2-2

UniProt

c.126C>A p.Asp42Glu missense variant moderate contig83 1803243

IGV: Start, Jump

G/T
NGS:
0.009
C90:
0.000
FAD2-2

UniProt

c.75C>A p.His25Gln missense variant moderate contig83 1803294

IGV: Start, Jump

G/T
NGS:
0.007
C90:
0.000
FAD2-2

UniProt

c.64G>T p.Ala22Ser missense variant moderate contig83 1803305

IGV: Start, Jump

C/A
NGS:
0.048
C90:
0.000
aPT4

UniProt

c.97T>C p.Tyr33His missense variant moderate contig121 2828753

IGV: Start, Jump

T/C
NGS:
0.439
C90:
0.000
aPT4

UniProt

c.235_236delGT p.Val79fs frameshift variant high contig121 2829030

IGV: Start, Jump

ATG/A
NGS:
0.417
C90:
0.000
aPT4

UniProt

c.238delT p.Ser80fs frameshift variant high contig121 2829034

IGV: Start, Jump

AT/A
NGS:
0.421
C90:
0.000
aPT4

UniProt

c.302A>G p.Asn101Ser missense variant moderate contig121 2829099

IGV: Start, Jump

A/G
NGS:
0.349
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.151G>T p.Ala51Ser missense variant moderate contig95 1989818

IGV: Start, Jump

G/T
NGS:
0.011
C90:
0.000
HDS-2

UniProt

c.509A>G p.Glu170Gly missense variant moderate contig95 1990365

IGV: Start, Jump

A/G
NGS:
0.002
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.083 0.167 0.250 0.333
clone distance sibling distance more distant
  1. 0.215 Tak-HN (RSP11618)
  2. 0.227 R3 (RSP11616)
  3. 0.247 R2 (RSP11615)
  4. 0.249 R1 (RSP11483)
  5. 0.276 Jiangji (RSP10653)
  6. 0.279 KYRG-151 (RSP11052)
  7. 0.282 KYRG-21 (RSP11053)
  8. 0.286 Squirrel Tail 31 (RSP11485)
  9. 0.292 Tisza (RSP10659)
  10. 0.293 Recon (RSP10755)
  11. 0.295 Santhica 27 (RSP10665)
  12. 0.295 Kyrgyz Gold (RSP11054)
  13. 0.296 Tisza (RSP11044)
  14. 0.296 Tygra (RSP10667)
  15. 0.296 KYRG-11 (RSP11051)
  16. 0.303 Lift (RSP11378)
  17. 0.304 Tisza (RSP11045)
  18. 0.306 Feral (RSP10891)
  19. 0.309 Santhica27 (RSP10056)
  20. 0.310 Santhica27 (RSP11046)

Nearest genetic relatives (Base Tree)

0 0.092 0.183 0.275 0.367
clone distance sibling distance more distant
  1. 0.271 Jiangji (RSP10653)
  2. 0.277 Tisza (RSP10659)
  3. 0.278 Tisza (RSP11044)
  4. 0.280 Tygra (RSP10667)
  5. 0.290 Kyrgyz Gold (RSP11054)
  6. 0.302 KYRG-11 (RSP11051)
  7. 0.307 Recon (RSP10755)
  8. 0.313 Santhica27 (RSP11047)
  9. 0.314 Monoica (RSP10241)
  10. 0.315 Ivory (RSP10668)
  11. 0.318 Futura 75 (RSP10664)
  12. 0.319 USO 31 (RSP10981)
  13. 0.321 Carmagnola (RSP10979)
  14. 0.321 Feral (RSP10890)
  15. 0.322 Fedora 17 (RSP10661)
  16. 0.323 Lovrin (RSP10658)
  17. 0.329 Carmagnola (RSP11037)
  18. 0.330 UP Sunrise (RSP10989)
  19. 0.334 Kimbo Slice (RSP10997)
  20. 0.347 RKM-2018-029 (RSP11121)

Most genetically distant strains (All Samples)

0 0.125 0.250 0.375 0.500
clone distance sibling distance more distant
  1. 0.491 Chem 91 (RSP11185)
  2. 0.463 Cherry Blossom (RSP11318)
  3. 0.460 RKM-2018-002 (RSP11093)
  4. 0.455 Dave Pineapple (RSP11626)
  5. 0.454 New York City Deisel (RSP11225)
  6. 0.450 Super Sour Diesel (RSP11191)
  7. 0.449 Chematonic Cannatonic x Chemdawg (RSP11394)
  8. 0.446 Queen Dream CBG (RSP11287)
  9. 0.445 Bordello (RSP11228)
  10. 0.443 QLE1 (RSP11451)
  11. 0.443 Cherry Blossom (RSP11323)
  12. 0.443 501st OG (RSP11241)
  13. 0.442 Escape Velocity (RSP11165)
  14. 0.442 Sour D (RSP11343)
  15. 0.441 Danny Noonan (RSP11070)
  16. 0.438 TI (RSP11149)
  17. 0.437 Mother s Milk No 31 (RSP11623)
  18. 0.437 QQD2 (RSP11450)
  19. 0.433 Medxotic (RSP11410)
  20. 0.432 OR (RSP10940)

Most genetically distant strains (Base Tree)

0 0.125 0.250 0.375 0.500
clone distance sibling distance more distant
  1. 0.468 RKM-2018-002 (RSP11093)
  2. 0.437 Hermaphrodite Research Sample1 (RSP11049)
  3. 0.436 RKM-2018-032 (RSP11124)
  4. 0.427 JL yellow (RSP11075)
  5. 0.426 Cbot-2019-001 (RSP11129)
  6. 0.425 Italian Kiss (RSP11034)
  7. 0.422 RKM-2018-018 (RSP11110)
  8. 0.421 Sour Raspberry (RSP10551)
  9. 0.421 RKM-2018-028 (RSP11120)
  10. 0.418 RKM-2018-006 (RSP11097)
  11. 0.418 Blue Dream (RSP11033)
  12. 0.416 RKM-2018-009 (RSP11100)
  13. 0.406 Skywalker OG (RSP10837)
  14. 0.401 CST (RSP11002)
  15. 0.397 Skunk 18 (RSP11038)
  16. 0.397 RKM-2018-005 (RSP11096)
  17. 0.397 RKM-2018-027 (RSP11119)
  18. 0.396 RKM-2018-022 (RSP11114)
  19. 0.394 RKM-2018-023 (RSP11115)
  20. 0.390 RKM-2018-026 (RSP11118)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4450138
Overlapping SNPs:
6
Concordance:
4

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495251
Overlapping SNPs:
3
Concordance:
3

Blockchain Registration Information

SHASUM Hash
cbb80119cdbafc14a9a1333bf8749660e62c2577897d493e498195fd44cc110b
QR code for RSP11617

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