Advanced Strain Search

USO 31

RSP 10983

Grower: John McKay-Colorado State University

General Information

Sample Name
USO31_1_1_CSU
Accession Date
July 16, 2017
Reported Plant Sex
Hermaphrodite

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 III

File Downloads

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: 1.09%
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: 0.0529
male female RSP10983

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.221C>G p.Thr74Ser missense variant moderate contig1772 2082447

IGV: Start, Jump

C/G
NGS:
0.136
C90:
0.057

Variants (Select Genes of Interest)
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.948T>G p.Asp316Glu missense variant moderate contig700 1950690

IGV: Start, Jump

A/C
NGS:
0.456
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-4b

UniProt

c.496A>G p.Lys166Glu missense variant moderate contig700 2721177

IGV: Start, Jump

T/C
NGS:
0.651
C90:
0.684
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.485A>G p.Lys162Arg missense variant moderate contig700 2721188

IGV: Start, Jump

T/C
NGS:
0.643
C90:
0.301
PKSG-4b

UniProt

c.431T>G p.Val144Gly missense variant moderate contig700 2721242

IGV: Start, Jump

A/C
NGS:
0.575
C90:
0.679
aPT1

UniProt

c.95_97delGTT p.Cys32del disruptive inframe deletion moderate contig121 2835800

IGV: Start, Jump

ATGT/A
NGS:
0.118
C90:
0.311
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.679G>C p.Gly227Arg missense variant moderate contig95 1990632

IGV: Start, Jump

G/C
NGS:
0.037
C90:
0.000

Nearest genetic relatives (All Samples)

clone distance sibling distance more distant
  1. 0.006 USO 31 (RSP10981)
  2. 0.136 Lovrin (RSP10658)
  3. 0.139 Carmagnola USO 31 (RSP11204)
  4. 0.150 USO31 (RSP10233)
  5. 0.172 Fedora 17 (RSP10661)
  6. 0.179 Santhica27 (RSP11046)
  7. 0.180 Santhica27 (RSP10056)
  8. 0.181 Santhica27 (RSP11047)
  9. 0.183 Fedora 17 (RSP11203)
  10. 0.185 Diana (RSP10235)
  11. 0.186 Tygra (RSP10667)
  12. 0.189 Ivory (RSP10668)
  13. 0.190 Monoica (RSP10241)
  14. 0.192 Futura 75 (RSP10664)
  15. 0.192 Santhica 27 (RSP10665)
  16. 0.213 KYRG-151 (RSP11052)
  17. 0.213 Tisza (RSP10659)
  18. 0.215 Carmagnola (RSP10982)
  19. 0.221 Carmagnola (RSP11037)
  20. 0.221 Carmagnola (RSP10977)

Nearest genetic relatives (Base Tree)

clone distance sibling distance more distant
  1. 0.006 USO 31 (RSP10981)
  2. 0.140 Lovrin (RSP10658)
  3. 0.173 Fedora 17 (RSP10661)
  4. 0.177 Santhica27 (RSP11047)
  5. 0.183 Ivory (RSP10668)
  6. 0.187 Monoica (RSP10241)
  7. 0.188 Futura 75 (RSP10664)
  8. 0.191 Tygra (RSP10667)
  9. 0.210 Tisza (RSP10659)
  10. 0.226 Carmagnola (RSP11037)
  11. 0.227 Tisza (RSP11044)
  12. 0.236 KYRG-11 (RSP11051)
  13. 0.242 Carmagnola (RSP10979)
  14. 0.244 Kyrgyz Gold (RSP11054)
  15. 0.249 Feral (RSP10890)
  16. 0.263 Jiangji (RSP10653)
  17. 0.287 RKM-2018-029 (RSP11121)
  18. 0.303 Recon (RSP10755)
  19. 0.304 Kimbo Slice (RSP10997)
  20. 0.312 Liberty Haze (RSP11000)

Most genetically distant strains (All Samples)

clone distance sibling distance more distant
  1. 0.475 Cherry Blossom (RSP11318)
  2. 0.461 Cherry Blossom (RSP11312)
  3. 0.455 Cherry Blossom (RSP11323)
  4. 0.446 Cherry Blossom (RSP11311)
  5. 0.445 Cherry Blossom (RSP11331)
  6. 0.443 Cherry Blossom (RSP11328)
  7. 0.441 Cherry Blossom (RSP11300)
  8. 0.439 Unknown- Cherry Wine - 001 (RSP11268)
  9. 0.438 Cherry Blossom (RSP11299)
  10. 0.438 Cherry Blossom (RSP11310)
  11. 0.437 Cherry Blossom (RSP11298)
  12. 0.430 Cherry Blossom (RSP11334)
  13. 0.430 Cherry Blossom (RSP11332)
  14. 0.430 Cherry Blossom (RSP11319)
  15. 0.427 Cherry Blossom (RSP11302)
  16. 0.427 Cherry Blossom (RSP11274)
  17. 0.425 Cherry Blossom (RSP11304)
  18. 0.424 Cherry Blossom (RSP11316)
  19. 0.424 Wife (RSP11148)
  20. 0.423 Cherry Blossom (RSP11308)

Most genetically distant strains (Base Tree)

clone distance sibling distance more distant
  1. 0.395 RKM-2018-002 (RSP11093)
  2. 0.386 Cbot-2019-005 (RSP11133)
  3. 0.375 Cherry (RSP11143)
  4. 0.372 RKM-2018-028 (RSP11120)
  5. 0.370 RKM-2018-006 (RSP11097)
  6. 0.365 JL yellow (RSP11075)
  7. 0.362 RKM-2018-023 (RSP11115)
  8. 0.362 Skunk 18 (RSP11038)
  9. 0.359 Cbot-2019-001 (RSP11129)
  10. 0.357 RKM-2018-032 (RSP11124)
  11. 0.356 RKM-2018-018 (RSP11110)
  12. 0.355 Cbot-2019-004 (RSP11132)
  13. 0.353 RKM-2018-022 (RSP11114)
  14. 0.353 Cherry (RSP11142)
  15. 0.351 RKM-2018-003 (RSP11094)
  16. 0.350 Hermaphrodite Research Sample1 (RSP11049)
  17. 0.349 Golden Goat 2 (RSP10991)
  18. 0.348 Blueberry Cheesecake (RSP10672)
  19. 0.348 UP Sunrise (RSP10989)
  20. 0.347 RKM-2018-027 (RSP11119)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4450090
Overlapping SNPs:
117
Concordance:
87

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495156
Overlapping SNPs:
7
Concordance:
6

Blockchain Registration Information

Transaction ID
aa2241bed437c94cbf06b5a718c45487bc25c2124a3235800e3a9ffa9b8db3c5
Stamping Certificate
Download PDF (856.9 KB)
SHASUM Hash
7772136e8bbb05033c7e1f4185e4766019378ad19913f564cb463d5655733e9a
QR code for RSP10983

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