VIR 483

SRR 14708238

Grower: Lanzhou University, Guangpeng Ren

General Information

Sample Name
UTT3
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 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: 1.34%
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: 0.0218
male female SRR14708238

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)

No variants to report

Variants (Select Genes of Interest)

PHL-2 c.1096G>A p.Ala366Thr missense variant moderate contig2621 340374

IGV: Start, Jump

G/A
NGS:
0.090
C90:
0.531
PHL-2 c.2783G>A p.Ser928Asn missense variant moderate contig2621 342826

IGV: Start, Jump

G/A
NGS:
0.107
C90:
0.890
PKSG-4a

UniProt

c.49_50insTGG p.Glu16_Gly17insVal disruptive inframe insertion moderate contig700 1936744

IGV: Start, Jump

A/AGGT
NGS:
0.013
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
DXR-2

UniProt

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

IGV: Start, Jump

A/G
NGS:
0.480
C90:
0.000
aPT1

UniProt

c.670T>A p.Ser224Thr missense variant moderate contig121 2840278

IGV: Start, Jump

T/A
NGS:
0.077
C90:
0.000
aPT1

UniProt

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

IGV: Start, Jump

C/G
NGS:
0.075
C90:
0.062
EMF1-1

UniProt

c.242A>G p.Lys81Arg missense variant moderate contig883 269731

IGV: Start, Jump

A/G
NGS:
0.022
C90:
0.053
aPT4

UniProt

c.198A>C p.Lys66Asn missense variant moderate contig121 2828854

IGV: Start, Jump

A/C
NGS:
0.044
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
GGR

UniProt

c.456T>A p.His152Gln missense variant moderate contig2282 549448

IGV: Start, Jump

T/A
NGS:
0.068
C90:
0.000
GGR

UniProt

c.460G>A p.Asp154Asn missense variant moderate contig2282 549452

IGV: Start, Jump

G/A
NGS:
0.070
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.042 0.083 0.125 0.167
clone distance sibling distance more distant
  1. 0.110 Lift (RSP11378)
  2. 0.112 AOAC MI 542 (RSP11755)
  3. 0.116 AOAC MI 597 (RSP11761)
  4. 0.118 Durban Poison 1 (RSP11013)
  5. 0.121 AOAC MI 588 (RSP11760)
  6. 0.123 AOAC MI 508 (RSP11750)
  7. 0.127 AOAC MI 545 (RSP11756)
  8. 0.127 AOAC MI 569 (RSP11759)
  9. 0.127 AOAC MI 535 (RSP11754)
  10. 0.129 Doug s Varin (RSP11243)
  11. 0.129 AOAC MI 532 (RSP11752)
  12. 0.129 AOAC MI 599 (RSP11762)
  13. 0.132 AOAC MI 501 (RSP11748)
  14. 0.132 AOAC MI 504 (RSP11749)
  15. 0.132 AOAC MI 533 (RSP11753)
  16. 0.133 Kompolti (SRR14708277)
  17. 0.134 Badger (RSP11614)
  18. 0.135 Durban Poison 1 (RSP10996)
  19. 0.138 Electra (RSP11366)
  20. 0.138 AOAC MI 548 (RSP11757)

Nearest genetic relatives (Base Tree)

0 0.067 0.133 0.200 0.267
clone distance sibling distance more distant
  1. 0.157 CST (RSP11002)
  2. 0.179 Durban Poison (RSP11014)
  3. 0.188 RKM-2018-019 (RSP11111)
  4. 0.194 Carmagnola (RSP10979)
  5. 0.196 Golden Goat 2 (RSP10991)
  6. 0.200 KYRG-11 (RSP11051)
  7. 0.204 Hermaphrodite ResearchSample2 (RSP11050)
  8. 0.206 Cbot-2019-001 (RSP11129)
  9. 0.207 RKM-2018-031 (RSP11123)
  10. 0.216 Recon (RSP10755)
  11. 0.221 Kyrgyz Gold (RSP11054)
  12. 0.221 RKM-2018-029 (RSP11121)
  13. 0.224 Blueberry Cheesecake (RSP10684)
  14. 0.227 Tygra (RSP10667)
  15. 0.229 Liberty Haze (RSP11000)
  16. 0.229 UP Sunrise (RSP10989)
  17. 0.231 Carmagnola (RSP11037)
  18. 0.233 Tisza (RSP10659)
  19. 0.238 Pie Hoe (RSP11073)
  20. 0.245 RKM-2018-026 (RSP11118)

Most genetically distant strains (All Samples)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.402 JL 4th Gen 4 (RSP11198)
  2. 0.400 JL 4th Gen 5 (RSP11199)
  3. 0.394 JL 4th Gen 6 (RSP11200)
  4. 0.388 JL yellow (RSP11075)
  5. 0.381 Chem 91 (RSP11185)
  6. 0.375 IUP3 (SRR14708256)
  7. 0.364 80E (RSP11213)
  8. 0.361 Feral (RSP11205)
  9. 0.357 JL 3rd Gen Mother (RSP11214)
  10. 0.357 JL 4th Gen 1 (RSP11193)
  11. 0.356 JL 3rd Gen Mother (RSP11197)
  12. 0.355 Squirrel Tail 81 (RSP11622)
  13. 0.353 Danny Noonan (RSP11070)
  14. 0.348 Sour Tsunami x Cataract Ku (RSP11183)
  15. 0.347 JL 4th Gen 2 (RSP11194)
  16. 0.347 JL 2 (RSP11076)
  17. 0.345 JL 3rd Gen Father (RSP11196)
  18. 0.339 Chematonic Cannatonic x Chemdawg (RSP11394)
  19. 0.337 AVIDEKEL 2 0 (RSP11174)
  20. 0.333 Northern Lights (RSP11501)

Most genetically distant strains (Base Tree)

0 0.092 0.183 0.275 0.367
clone distance sibling distance more distant
  1. 0.361 RKM-2018-002 (RSP11093)
  2. 0.361 JL yellow (RSP11075)
  3. 0.329 Ivory (RSP10668)
  4. 0.329 Skunk 18 (RSP11038)
  5. 0.319 RKM-2018-033 (RSP11125)
  6. 0.313 Blue Dream (RSP11033)
  7. 0.310 Kush Hemp E1 (RSP11128)
  8. 0.308 USO 31 (RSP10981)
  9. 0.305 Cherry (RSP11142)
  10. 0.303 RKM-2018-018 (RSP11110)
  11. 0.296 Fedora 17 (RSP10661)
  12. 0.293 RKM-2018-027 (RSP11119)
  13. 0.292 The Gift (RSP10988)
  14. 0.290 Skywalker OG (RSP10837)
  15. 0.289 Futura 75 (RSP10664)
  16. 0.289 Cbot-2019-005 (RSP11133)
  17. 0.289 Jiangji (RSP10653)
  18. 0.287 RKM-2018-006 (RSP11097)
  19. 0.286 RKM-2018-028 (RSP11120)
  20. 0.285 RKM-2018-005 (RSP11096)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4451181
Overlapping SNPs:
6
Concordance:
6

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495242
Overlapping SNPs:
2
Concordance:
2
QR code for SRR14708238

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