Advanced Strain Search

JL_X_NSPM1_21

RSP 11474

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: 0.94%
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: 0.0810
male female RSP11474

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.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
DXR-2

UniProt

c.431C>G p.Ala144Gly missense variant moderate contig380 287760

IGV: Start, Jump

G/C
NGS:
0.182
C90:
0.550
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.775delT p.Tyr259fs frameshift variant high contig121 2831380

IGV: Start, Jump

AT/A
NGS:
0.224
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.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
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
HDS-1

UniProt

c.-108+1_-108+2insG splice donor variant & intron variant high contig1891 889975

IGV: Start, Jump

A/AC
NGS:
0.217
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.033 0.067 0.100 0.133
closely related moderately related distantly related
  1. 0.048 JL X NSPM1 14 (RSP11473)
  2. 0.071 JL X NSPM1 30 (RSP11476)
  3. 0.073 JL Cross 18 (RSP11519)
  4. 0.076 JL X NSPM1 7 (RSP11469)
  5. 0.078 JL Cross 23 (RSP11524)
  6. 0.092 JL Cross 22 (RSP11523)
  7. 0.093 JL X NSPM1 33 (RSP11477)
  8. 0.096 JL Tent 2 (RSP11489)
  9. 0.099 JL Cross 17 (RSP11518)
  10. 0.101 JL Cross 19 (RSP11520)
  11. 0.101 JL Tent 3 (RSP11490)
  12. 0.102 JL X NSPM1 22 (RSP11475)
  13. 0.103 JL x NSPM1 3 (RSP11481)
  14. 0.107 JL Cross 28 (RSP11529)
  15. 0.108 JL Cross 21 (RSP11522)
  16. 0.108 JL X NSPM1 5 (RSP11467)
  17. 0.113 JL Tent 4 (RSP11491)
  18. 0.114 JL x NSPM1 1 5 (RSP11479)
  19. 0.116 JL Cross 9 (RSP11510)
  20. 0.120 JL Cross 15 (RSP11516)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
closely related moderately related distantly related
  1. 0.464 80E (RSP11213)
  2. 0.436 Cbot-2019-005 (RSP11133)
  3. 0.430 80E (RSP11211)
  4. 0.430 CS (RSP11208)
  5. 0.427 Arcata Trainwreck (RSP11176)
  6. 0.425 Northern Lights (RSP11501)
  7. 0.424 R1in136 (SRR14708226)
  8. 0.423 80E (RSP11212)
  9. 0.423 Carmagnola (RSP11202)
  10. 0.420 R1in136 (SRR14708237)
  11. 0.419 Cherry Blossom (RSP11323)
  12. 0.419 Ruderalis Indica (SRR14708267)
  13. 0.416 IUP3 (SRR14708256)
  14. 0.413 R1in136 (SRR14708227)
  15. 0.412 Carmaleonte (RSP11207)
  16. 0.412 IUP2 (SRR14708257)
  17. 0.412 Tanao Sri -46- (RSP11486)
  18. 0.411 Feral (RSP11205)
  19. 0.409 IBE (SRR14708228)
  20. 0.408 XBL1 (SRR14708207)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR8349319
Overlapping SNPs:
68
Concordance:
42

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495248
Overlapping SNPs:
2
Concordance:
2

Blockchain Registration Information

Transaction ID
f9dc6b520c512525268c1478d9c2a98119709f457aee5f34aa8bc16d13fe22de
Stamping Certificate
Download PDF (39.7 KB)
SHASUM Hash
2955606a4a3184e68d2cfbaaaa9be74ac86742174493bebbf0814ed496cb0dc4
QR code for RSP11474

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