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JL_X_NSPM1_7

RSP 11469

Grower: Kevin McKernan

General Information

Accession Date
May 7, 2020
Reported Plant Sex
Male
DNA Extracted From
Stem

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

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: 0.92%
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: 0.0834
male female RSP11469

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
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)
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.31A>T p.Thr11Ser missense variant moderate contig700 1951851

IGV: Start, Jump

T/A
NGS:
0.844
C90:
0.880
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.523C>A p.His175Asn missense variant moderate contig700 2721150

IGV: Start, Jump

G/T
NGS:
0.002
C90:
0.000
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.353_354insCC p.Gly119fs frameshift variant high contig700 2721319

IGV: Start, Jump

T/TGG
NGS:
0.175
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
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.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
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 0.033 0.067 0.100 0.133
closely related moderately related distantly related
  1. 0.046 JL X NSPM1 14 (RSP11473)
  2. 0.047 JL Tent 2 (RSP11489)
  3. 0.049 JL Cross 21 (RSP11522)
  4. 0.056 JL Cross 19 (RSP11520)
  5. 0.058 JL Tent 3 (RSP11490)
  6. 0.059 JL Cross 17 (RSP11518)
  7. 0.062 JL Cross 23 (RSP11524)
  8. 0.069 JL Cross 9 (RSP11510)
  9. 0.076 JL X NSPM1 21 (RSP11474)
  10. 0.077 JL Cross 18 (RSP11519)
  11. 0.079 JL Cross 28 (RSP11529)
  12. 0.079 JL Cross 26 (RSP11527)
  13. 0.082 JL X NSPM1 11 (RSP11471)
  14. 0.086 JL x NSPM1 1 5 (RSP11479)
  15. 0.091 JL Cross 24 (RSP11525)
  16. 0.097 JL Cross 22 (RSP11523)
  17. 0.098 JL x NSPM1 1 (RSP11478)
  18. 0.101 JL x NSPM1 3 (RSP11481)
  19. 0.103 JL Tent 4 (RSP11491)
  20. 0.103 JL Cross 27 (RSP11528)

Most genetically distant strains (All Samples)

0 0.108 0.217 0.325 0.433
closely related moderately related distantly related
  1. 0.430 80E (RSP11213)
  2. 0.402 Northern Lights (RSP11501)
  3. 0.400 BagSeed (RSP12627)
  4. 0.400 80E (RSP11211)
  5. 0.398 R1in136 (SRR14708226)
  6. 0.396 Cherry Blossom (RSP11323)
  7. 0.395 R3in134 (SRR14708218)
  8. 0.395 80E (RSP11212)
  9. 0.394 R1in136 (SRR14708227)
  10. 0.394 IUP3 (SRR14708256)
  11. 0.392 CS (RSP11208)
  12. 0.390 IUP2 (SRR14708257)
  13. 0.389 Juso14 (SRR14708259)
  14. 0.389 Tanao Sri -46- (RSP11486)
  15. 0.389 R3in134 (SRR14708235)
  16. 0.389 VIR 223 - Bernburgskaya Odnodomnaya - bm (SRR14708217)
  17. 0.389 R1in136 (SRR14708237)
  18. 0.388 R3in134 (SRR14708220)
  19. 0.388 Cbot-2019-005 (RSP11133)
  20. 0.387 Santhica27 (RSP10056)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448214
Overlapping SNPs:
60
Concordance:
39

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495303
Overlapping SNPs:
2
Concordance:
2

Blockchain Registration Information

Transaction ID
9b1ec1d0c577d980eeed6e8e149e13a149e340f177e2536323b3f9fbf65f96b1
Stamping Certificate
Download PDF (39.9 KB)
SHASUM Hash
669427f525fc3209abf68316d202d1ce939637ac7d445fb39a6873959b1b32c6
QR code for RSP11469

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