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JL_x_NSPM1_2

RSP 11480

Grower: Kevin McKernan

General Information

Accession Date
May 7, 2020
Reported Plant Sex
Female
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: 0.8%
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: 0.0384
male female RSP11480

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.781T>A p.Leu261Ile missense variant moderate contig700 1944609

IGV: Start, Jump

A/T
NGS:
0.026
C90:
0.574
PKSG-2a

UniProt

c.774G>A p.Met258Ile missense variant moderate contig700 1944616

IGV: Start, Jump

C/T
NGS:
0.123
C90:
0.000
PKSG-2a

UniProt

c.241G>A p.Val81Met missense variant moderate contig700 1945149

IGV: Start, Jump

C/T
NGS:
0.136
C90:
0.000
PKSG-2a

UniProt

c.240T>G p.Asp80Glu missense variant moderate contig700 1945150

IGV: Start, Jump

A/C
NGS:
0.136
C90:
0.000
PKSG-2a

UniProt

c.230T>C p.Val77Ala missense variant moderate contig700 1945160

IGV: Start, Jump

A/G
NGS:
0.114
C90:
0.000
PKSG-2a

UniProt

c.224A>G p.Lys75Arg missense variant moderate contig700 1945166

IGV: Start, Jump

T/C
NGS:
0.143
C90:
0.962
PKSG-2a

UniProt

c.188T>G p.Ile63Ser missense variant moderate contig700 1945202

IGV: Start, Jump

A/C
NGS:
0.101
C90:
0.000
PKSG-2a

UniProt

c.188T>A p.Ile63Asn missense variant moderate contig700 1945202

IGV: Start, Jump

A/T
NGS:
0.061
C90:
0.000
PKSG-2a

UniProt

c.187A>T p.Ile63Phe missense variant moderate contig700 1945203

IGV: Start, Jump

T/A
NGS:
0.101
C90:
0.000
PKSG-2a

UniProt

c.167C>G p.Thr56Ser missense variant moderate contig700 1945223

IGV: Start, Jump

G/C
NGS:
0.075
C90:
0.000
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.774G>A p.Met258Ile missense variant moderate contig700 1950864

IGV: Start, Jump

C/T
NGS:
0.366
C90:
0.947
PKSG-2b

UniProt

c.241G>A p.Val81Met missense variant moderate contig700 1951397

IGV: Start, Jump

C/T
NGS:
0.154
C90:
0.000
PKSG-2b

UniProt

c.240T>G p.Asp80Glu missense variant moderate contig700 1951398

IGV: Start, Jump

A/C
NGS:
0.156
C90:
0.000
PKSG-2b

UniProt

c.230T>C p.Val77Ala missense variant moderate contig700 1951408

IGV: Start, Jump

A/G
NGS:
0.134
C90:
0.646
PKSG-2b

UniProt

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

IGV: Start, Jump

T/A
NGS:
0.844
C90:
0.880
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

Nearest genetic relatives (All Samples)

0 0.050 0.100 0.150 0.200
closely related moderately related distantly related
  1. 0.107 JL X NSPM1 5 (RSP11467)
  2. 0.108 JL Cross 7 (RSP11508)
  3. 0.111 JL Cross 15 (RSP11516)
  4. 0.120 JL X NSPM1 11 (RSP11471)
  5. 0.124 JL Cross 24 (RSP11525)
  6. 0.125 JL X NSPM1 22 (RSP11475)
  7. 0.128 JL Cross 22 (RSP11523)
  8. 0.135 JL x NSPM1 1 5 (RSP11479)
  9. 0.142 JL Tent 1 yellow stake (RSP11488)
  10. 0.145 JL Cross 26 (RSP11527)
  11. 0.150 JL Cross 27 (RSP11528)
  12. 0.152 JL X NSPM1 33 (RSP11477)
  13. 0.158 JL X NSPM1 7 (RSP11469)
  14. 0.159 Blue Dream (RSP11004)
  15. 0.160 JL X NSPM1 14 (RSP11473)
  16. 0.161 JL x NSPM1 3 (RSP11481)
  17. 0.164 JL Cross 2 (RSP11503)
  18. 0.164 JL Cross 21 (RSP11522)
  19. 0.168 Domnesia (RSP11184)
  20. 0.168 JL Cross 23 (RSP11524)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
closely related moderately related distantly related
  1. 0.463 80E (RSP11213)
  2. 0.440 Kush Hemp E1 (RSP11128)
  3. 0.439 CS (RSP11208)
  4. 0.435 80E (RSP11212)
  5. 0.435 BagSeed (RSP12627)
  6. 0.434 80E (RSP11211)
  7. 0.433 Cbot-2019-005 (RSP11133)
  8. 0.433 R1in136 (SRR14708226)
  9. 0.426 R1in136 (SRR14708227)
  10. 0.425 IUP3 (SRR14708256)
  11. 0.424 Feral (RSP11205)
  12. 0.422 Carmaleonte (RSP11207)
  13. 0.422 Carmagnola (RSP11202)
  14. 0.421 R1in136 (SRR14708237)
  15. 0.418 IUP2 (SRR14708257)
  16. 0.418 Juso14 (SRR14708259)
  17. 0.417 Fatso (RSP11741)
  18. 0.416 Tanao Sri-white -80- (RSP11621)
  19. 0.415 Feral (RSP10891)
  20. 0.412 Feral (RSP10892)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR8349115
Overlapping SNPs:
68
Concordance:
42

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495303
Overlapping SNPs:
2
Concordance:
2

Blockchain Registration Information

Transaction ID
60a7da30caadc5cba429dd9e1e3259e07c7d503517a04a2f1552d3b58b33f2a6
Stamping Certificate
Download PDF (39.8 KB)
SHASUM Hash
fb35583e98d12e05bd2586a8011c059cf3561a8eac1b7561ea4fc6e1bf46b953
QR code for RSP11480

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