Wild Thailand

SRR 14708216

Grower: Lanzhou University, Guangpeng Ren

General Information

Sample Name
THD
Accession Date
May 31, 2021
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: Common
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: 1.34%
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: 0.0573
male female SRR14708216

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)

THCAS c.1229G>A p.Gly410Glu missense variant moderate contig741 4416599

IGV: Start, Jump

C/T
NGS:
0.039
C90:
0.000
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)

PHL-2 c.455A>C p.Asp152Ala missense variant moderate contig2621 339191

IGV: Start, Jump

A/C
NGS:
0.018
C90:
0.507
PHL-2 c.977A>C p.His326Pro missense variant moderate contig2621 340255

IGV: Start, Jump

A/C
NGS:
0.007
C90:
0.000
PHL-2 c.1057A>G p.Arg353Gly missense variant moderate contig2621 340335

IGV: Start, Jump

A/G
NGS:
0.096
C90:
0.555
PHL-2 c.1540A>G p.Thr514Ala missense variant moderate contig2621 340818

IGV: Start, Jump

A/G
NGS:
0.042
C90:
0.282
PHL-2 c.3467A>G p.Gln1156Arg missense variant moderate contig2621 343510

IGV: Start, Jump

A/G
NGS:
0.064
C90:
0.713
OAC-2

UniProt

c.22G>A p.Val8Ile missense variant moderate contig931 110317

IGV: Start, Jump

C/T
NGS:
0.018
C90:
0.000
ELF3

UniProt

c.358G>A p.Gly120Arg missense variant moderate contig97 242064

IGV: Start, Jump

G/A
NGS:
0.099
C90:
0.493
ELF3

UniProt

c.772A>G p.Ser258Gly missense variant moderate contig97 242478

IGV: Start, Jump

A/G
NGS:
0.112
C90:
0.000
ELF3

UniProt

c.1230-2_1230-1delAG splice acceptor variant & intron variant high contig97 243676

IGV: Start, Jump

TAG/T
NGS:
0.088
C90:
0.450
ELF3

UniProt

c.1630A>G p.Thr544Ala missense variant moderate contig97 244461

IGV: Start, Jump

A/G
NGS:
0.103
C90:
0.545
ELF3

UniProt

c.1966C>G p.Pro656Ala missense variant moderate contig97 244797

IGV: Start, Jump

C/G
NGS:
0.123
C90:
0.632
ELF3

UniProt

c.2141C>G p.Pro714Arg missense variant moderate contig97 244972

IGV: Start, Jump

C/G
NGS:
0.088
C90:
0.335
ELF3

UniProt

c.2198G>T p.Arg733Leu missense variant moderate contig97 245029

IGV: Start, Jump

G/T
NGS:
0.125
C90:
0.531
ELF5

UniProt

c.853C>T p.Pro285Ser missense variant moderate contig382 880715

IGV: Start, Jump

C/T
NGS:
0.007
C90:
0.153
aPT1

UniProt

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

IGV: Start, Jump

A/G
NGS:
0.579
C90:
0.761
aPT1

UniProt

c.629C>T p.Thr210Ile missense variant moderate contig121 2840237

IGV: Start, Jump

C/T
NGS:
0.561
C90:
0.598
aPT1

UniProt

c.864C>G p.Asn288Lys missense variant moderate contig121 2842407

IGV: Start, Jump

C/G
NGS:
0.075
C90:
0.062
AAE1-2

UniProt

c.688G>A p.Asp230Asn missense variant moderate contig81 209650

IGV: Start, Jump

G/A
NGS:
0.018
C90:
0.000
AAE1-2

UniProt

c.1415G>A p.Ser472Asn missense variant moderate contig81 210377

IGV: Start, Jump

G/A
NGS:
0.070
C90:
0.000
AAE1-2

UniProt

c.1434G>T p.Glu478Asp missense variant moderate contig81 210396

IGV: Start, Jump

G/T
NGS:
0.075
C90:
0.000
PKSG-2b

UniProt

c.948T>G p.Asp316Glu missense variant moderate contig700 1950690

IGV: Start, Jump

A/C
NGS:
0.456
C90:
0.000
PKSG-2b

UniProt

c.945T>G p.Ser315Arg missense variant moderate contig700 1950693

IGV: Start, Jump

A/C
NGS:
0.454
C90:
0.000
PKSG-2b

UniProt

c.944G>A p.Ser315Asn missense variant moderate contig700 1950694

IGV: Start, Jump

C/T
NGS:
0.445
C90:
0.000
PKSG-2b

UniProt

c.934C>G p.His312Asp missense variant moderate contig700 1950704

IGV: Start, Jump

G/C
NGS:
0.410
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
TFL1

UniProt

c.302-1G>A splice acceptor variant & intron variant high contig1636 520616

IGV: Start, Jump

C/T
NGS:
0.103
C90:
0.794
HDS-1

UniProt

c.1618A>G p.Ile540Val missense variant moderate contig1891 885936

IGV: Start, Jump

T/C
NGS:
0.099
C90:
0.861
HDS-1

UniProt

c.136G>A p.Val46Ile missense variant moderate contig1891 889256

IGV: Start, Jump

C/T
NGS:
0.088
C90:
0.593
HDS-1

UniProt

c.56C>G p.Ala19Gly missense variant moderate contig1891 889336

IGV: Start, Jump

G/C
NGS:
0.125
C90:
0.943
HDS-1

UniProt

c.35G>A p.Cys12Tyr missense variant moderate contig1891 889357

IGV: Start, Jump

C/T
NGS:
0.094
C90:
0.646
PIE1-2

UniProt

c.710C>T p.Pro237Leu missense variant moderate contig1460 1193804

IGV: Start, Jump

G/A
NGS:
0.072
C90:
0.866
PIE1-2

UniProt

c.706T>C p.Tyr236His missense variant moderate contig1460 1193808

IGV: Start, Jump

A/G
NGS:
0.059
C90:
0.737
EMF2

UniProt

c.1772A>G p.Gln591Arg missense variant moderate contig954 3059929

IGV: Start, Jump

A/G
NGS:
0.092
C90:
0.876
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.153A>C p.Lys51Asn missense variant moderate contig121 2828809

IGV: Start, Jump

A/C
NGS:
0.375
C90:
0.000
aPT4

UniProt

c.235_237delGTA p.Val79del conservative inframe deletion moderate contig121 2829031

IGV: Start, Jump

TGTA/T
NGS:
0.002
C90:
0.000
FLD

UniProt

c.2686G>A p.Ala896Thr missense variant moderate contig1450 2044848

IGV: Start, Jump

C/T
NGS:
0.035
C90:
0.225
FLD

UniProt

c.2681T>C p.Ile894Thr missense variant moderate contig1450 2044853

IGV: Start, Jump

A/G
NGS:
0.020
C90:
0.144
AAE1-3

UniProt

c.722G>A p.Arg241Lys missense variant moderate contig976 1083132

IGV: Start, Jump

C/T
NGS:
0.070
C90:
0.000
AAE1-3

UniProt

c.382T>C p.Tyr128His missense variant moderate contig976 1083643

IGV: Start, Jump

A/G
NGS:
0.072
C90:
0.000
AAE1-3

UniProt

c.293A>G p.Asp98Gly missense variant moderate contig976 1083732

IGV: Start, Jump

T/C
NGS:
0.068
C90:
0.000
AAE1-3

UniProt

c.125A>G p.Glu42Gly missense variant moderate contig976 1083950

IGV: Start, Jump

T/C
NGS:
0.064
C90:
0.000
AAE1-3

UniProt

c.104T>C p.Leu35Pro missense variant moderate contig976 1083971

IGV: Start, Jump

A/G
NGS:
0.009
C90:
0.000
GGR

UniProt

c.362A>T p.Tyr121Phe missense variant moderate contig2282 549354

IGV: Start, Jump

A/T
NGS:
0.029
C90:
0.000
GGR

UniProt

c.704A>T p.His235Leu missense variant moderate contig2282 549696

IGV: Start, Jump

A/T
NGS:
0.121
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.042 0.083 0.125 0.167
clone distance sibling distance more distant
  1. 0.128 AOAC MI 597 (RSP11761)
  2. 0.129 AOAC MI 588 (RSP11760)
  3. 0.130 AOAC MI 569 (RSP11759)
  4. 0.131 B52 (SRR14708255)
  5. 0.132 Lift (RSP11378)
  6. 0.132 Durban Poison 1 (RSP11013)
  7. 0.132 Electra (RSP11366)
  8. 0.132 Doug s Varin (RSP11243)
  9. 0.133 AOAC MI 501 (RSP11748)
  10. 0.133 AOAC MI 542 (RSP11755)
  11. 0.135 AOAC MI 533 (RSP11753)
  12. 0.136 AOAC MI 545 (RSP11756)
  13. 0.136 AOAC MI 567 (RSP11758)
  14. 0.137 AOAC MI 504 (RSP11749)
  15. 0.140 AOAC MI 599 (RSP11762)
  16. 0.141 AOAC MI 548 (RSP11757)
  17. 0.144 AOAC MI 532 (RSP11752)
  18. 0.149 Blue Dream (RSP11010)
  19. 0.150 AOAC MI 508 (RSP11750)
  20. 0.151 AOAC MI 535 (RSP11754)

Nearest genetic relatives (Base Tree)

0 0.075 0.150 0.225 0.300
clone distance sibling distance more distant
  1. 0.173 UP Sunrise (RSP10989)
  2. 0.176 Liberty Haze (RSP11000)
  3. 0.197 Gold Cracker (RSP11048)
  4. 0.207 RKM-2018-022 (RSP11114)
  5. 0.212 The Gift (RSP10988)
  6. 0.214 Blueberry Cheesecake (RSP10684)
  7. 0.217 RKM-2018-019 (RSP11111)
  8. 0.227 Jiangji (RSP10653)
  9. 0.227 Recon (RSP10755)
  10. 0.230 RKM-2018-027 (RSP11119)
  11. 0.239 Golden Goat 2 (RSP10991)
  12. 0.240 Tisza (RSP10659)
  13. 0.242 Cbot-2019-006 (RSP11134)
  14. 0.243 KYRG-11 (RSP11051)
  15. 0.250 Durban Poison (RSP11014)
  16. 0.250 Hermaphrodite ResearchSample2 (RSP11050)
  17. 0.264 Pie Hoe (RSP11073)
  18. 0.266 RKM-2018-029 (RSP11121)
  19. 0.273 RKM-2018-031 (RSP11123)
  20. 0.276 RKM-2018-009 (RSP11100)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.453 JL yellow (RSP11075)
  2. 0.425 JL 3rd Gen Mother (RSP11214)
  3. 0.418 Danny Noonan (RSP11070)
  4. 0.408 JL 4th Gen 5 (RSP11199)
  5. 0.408 80E (RSP11213)
  6. 0.403 Ivory (RSP10668)
  7. 0.396 R1in136 (SRR14708226)
  8. 0.396 80E (RSP11211)
  9. 0.394 JL 3rd Gen Mother (RSP11197)
  10. 0.387 Cherry Blossom (RSP11323)
  11. 0.387 Tanao Sri-white 80 (RSP11621)
  12. 0.386 JL 4th Gen 1 (RSP11193)
  13. 0.382 CS (RSP11208)
  14. 0.378 Feral (RSP11206)
  15. 0.376 Carmagnola (RSP11202)
  16. 0.376 Carmaleonte (RSP11207)
  17. 0.372 JL 3rd Gen Father (RSP11196)
  18. 0.371 Tiger Tail 30 (RSP11484)
  19. 0.366 80E (RSP11212)
  20. 0.364 JL 4th Gen 4 (RSP11198)

Most genetically distant strains (Base Tree)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.447 JL yellow (RSP11075)
  2. 0.416 Ivory (RSP10668)
  3. 0.395 Carmagnola (RSP10979)
  4. 0.360 Cbot-2019-004 (RSP11132)
  5. 0.359 Lovrin (RSP10658)
  6. 0.352 Black Beauty (RSP11035)
  7. 0.352 Kush Hemp E1 (RSP11128)
  8. 0.347 Cbot-2019-005 (RSP11133)
  9. 0.345 Carmagnola (RSP11037)
  10. 0.340 Santhica27 (RSP11047)
  11. 0.337 Fedora 17 (RSP10661)
  12. 0.333 Feral (RSP10890)
  13. 0.331 Sour Raspberry (RSP10551)
  14. 0.331 RKM-2018-033 (RSP11125)
  15. 0.329 Futura 75 (RSP10664)
  16. 0.326 Monoica (RSP10241)
  17. 0.325 RKM-2018-002 (RSP11093)
  18. 0.323 RKM-2018-026 (RSP11118)
  19. 0.320 Blueberry Cheesecake (RSP10672)
  20. 0.320 Skywalker OG (RSP10837)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR8346980
Overlapping SNPs:
17
Concordance:
14

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495200
Overlapping SNPs:
4
Concordance:
4
QR code for SRR14708216

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