Advanced Strain Search

USO31

RSP 10233

Grower: CSU

General Information

Sample Name
USO31-3
Accession Date
May 12, 2016
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 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: 1.21%
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: 0.0520
male female RSP10233

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

IGV: Start, Jump

A/T
NGS:
0.715
C90:
0.895
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
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
PKSG-4b

UniProt

c.419A>G p.Asp140Gly missense variant moderate contig700 2721254

IGV: Start, Jump

T/C
NGS:
0.430
C90:
0.440
aPT4

UniProt

c.470T>C p.Leu157Ser missense variant moderate contig121 2830665

IGV: Start, Jump

T/C
NGS:
0.007
C90:
0.000
aPT4

UniProt

c.517A>T p.Ile173Leu missense variant & splice region variant moderate contig121 2830795

IGV: Start, Jump

A/T
NGS:
0.022
C90:
0.000
aPT4

UniProt

c.1168T>C p.Tyr390His missense variant moderate contig121 2833503

IGV: Start, Jump

T/C
NGS:
0.546
C90:
0.000
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
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.715G>C p.Ala239Pro missense variant moderate contig121 2841350

IGV: Start, Jump

G/C
NGS:
0.004
C90:
0.000
aPT1

UniProt

c.727G>T p.Glu243* stop gained high contig121 2841362

IGV: Start, Jump

G/T
NGS:
0.127
C90:
0.100
aPT1

UniProt

c.958G>A p.Gly320Ser missense variant moderate contig121 2842731

IGV: Start, Jump

G/A
NGS:
0.004
C90:
0.000
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. 0.150 USO 31 (RSP10983)
  2. 0.158 USO 31 (RSP10981)
  3. 0.162 Lovrin (RSP10658)
  4. 0.165 Santhica 27 (RSP10665)
  5. 0.177 Santhica27 (RSP10056)
  6. 0.186 Santhica27 (RSP11046)
  7. 0.189 Tygra (RSP10667)
  8. 0.193 Santhica27 (RSP11047)
  9. 0.195 Monoica (RSP10241)
  10. 0.196 Fedora 17 (RSP10661)
  11. 0.198 Futura 75 (RSP10664)
  12. 0.198 Fedora 17 (RSP11203)
  13. 0.200 Carmagnola USO 31 (RSP11204)
  14. 0.213 Ivory (RSP10668)
  15. 0.214 Diana (RSP10235)
  16. 0.214 Carmaleonte (RSP11207)
  17. 0.221 Tisza (RSP10659)
  18. 0.229 KYRG-21 (RSP11053)
  19. 0.230 Carmagnola (RSP10978)
  20. 0.231 Carmagnola (RSP10976)

Nearest genetic relatives (Base Tree)

0 0.083 0.167 0.250 0.333
clone distance sibling distance more distant
  1. 0.165 USO 31 (RSP10981)
  2. 0.176 Lovrin (RSP10658)
  3. 0.189 Monoica (RSP10241)
  4. 0.195 Tygra (RSP10667)
  5. 0.196 Santhica27 (RSP11047)
  6. 0.197 Futura 75 (RSP10664)
  7. 0.199 Fedora 17 (RSP10661)
  8. 0.203 Ivory (RSP10668)
  9. 0.224 Tisza (RSP10659)
  10. 0.235 Tisza (RSP11044)
  11. 0.243 Carmagnola (RSP10979)
  12. 0.250 Carmagnola (RSP11037)
  13. 0.253 Kyrgyz Gold (RSP11054)
  14. 0.257 KYRG-11 (RSP11051)
  15. 0.261 Jiangji (RSP10653)
  16. 0.263 Feral (RSP10890)
  17. 0.312 RKM-2018-029 (RSP11121)
  18. 0.323 Kimbo Slice (RSP10997)
  19. 0.323 Recon (RSP10755)
  20. 0.325 RKM-2018-034 (RSP11126)

Most genetically distant strains (All Samples)

0 0.125 0.250 0.375 0.500
clone distance sibling distance more distant
  1. 0.468 Cherry Blossom (RSP11312)
  2. 0.460 Cherry Blossom (RSP11318)
  3. 0.459 Cherry Blossom (RSP11323)
  4. 0.451 Cherry Blossom (RSP11300)
  5. 0.451 Cherry Blossom (RSP11331)
  6. 0.450 Cherry Blossom (RSP11311)
  7. 0.449 Cherry Blossom (RSP11301)
  8. 0.438 Cherry Blossom (RSP11315)
  9. 0.435 Cherry Blossom (RSP11298)
  10. 0.434 Cherry Blossom (RSP11325)
  11. 0.434 Cherry Blossom (RSP11308)
  12. 0.433 Cherry Blossom (RSP11319)
  13. 0.433 Cherry Blossom (RSP11299)
  14. 0.433 Cherry Blossom (RSP11322)
  15. 0.433 Cherry Blossom (RSP11334)
  16. 0.432 Cherry Blossom (RSP11306)
  17. 0.432 Cherry Blossom (RSP11335)
  18. 0.430 Cherry Blossom (RSP11327)
  19. 0.430 Cherry Blossom (RSP11332)
  20. 0.428 Cherry Blossom (RSP11316)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.397 Cbot-2019-005 (RSP11133)
  2. 0.388 Cbot-2019-001 (RSP11129)
  3. 0.385 RKM-2018-028 (RSP11120)
  4. 0.378 RKM-2018-018 (RSP11110)
  5. 0.377 Cherry (RSP11143)
  6. 0.373 JL yellow (RSP11075)
  7. 0.372 UP Sunrise (RSP10989)
  8. 0.372 Skunk 18 (RSP11038)
  9. 0.371 Hermaphrodite Research Sample1 (RSP11049)
  10. 0.371 RKM-2018-006 (RSP11097)
  11. 0.369 RKM-2018-002 (RSP11093)
  12. 0.368 RKM-2018-022 (RSP11114)
  13. 0.368 RKM-2018-003 (RSP11094)
  14. 0.367 Cbot-2019-004 (RSP11132)
  15. 0.363 Cherry (RSP11142)
  16. 0.363 RKM-2018-019 (RSP11111)
  17. 0.362 RKM-2018-023 (RSP11115)
  18. 0.358 Gold Cracker (RSP11048)
  19. 0.357 RKM-2018-032 (RSP11124)
  20. 0.356 RKM-2018-009 (RSP11100)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4450090
Overlapping SNPs:
123
Concordance:
88

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495194
Overlapping SNPs:
11
Concordance:
10

Blockchain Registration Information

Transaction ID
3a666144f2508230dd6174634d65a30b35988ca82942d9c0401a4b90b09289eb
Stamping Certificate
Download PDF (864.3 KB)
SHASUM Hash
0cd30ec577accaf5c07e0c2141ab2ee0f252ef8c4e97e75bb9205e0417de9c54
QR code for RSP10233

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