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Carmagnola

RSP 10978

Grower: John McKay-Colorado State University

General Information

Sample Name
Carm_3_2_CSU
Accession Date
July 16, 2017
Reported Plant Sex
Female
DNA Extracted From
Unknown

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: 0.0519
male female RSP10978

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)

No variants to report

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

IGV: Start, Jump

T/A
NGS:
0.844
C90:
0.880
aPT4

UniProt

c.757G>T p.Val253Leu missense variant moderate contig121 2831364

IGV: Start, Jump

G/T
NGS:
0.039
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.574A>T p.Met192Leu missense variant moderate contig121 2840182

IGV: Start, Jump

A/T
NGS:
0.024
C90:
0.000
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.727G>T p.Glu243* stop gained high contig121 2841362

IGV: Start, Jump

G/T
NGS:
0.127
C90:
0.100
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.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)

0 0.058 0.117 0.175 0.233
closely related moderately related distantly related
  1. 0.003 Carmagnola (RSP10979)
  2. 0.003 Carmagnola (RSP10976)
  3. 0.008 Carmagnola (RSP11202)
  4. 0.112 Carmagnola (RSP10655)
  5. 0.136 Carmagnola (RSP10982)
  6. 0.145 Carmagnola (RSP11039)
  7. 0.145 Carmagnola (RSP11037)
  8. 0.146 Carmagnola (RSP10980)
  9. 0.151 Carmagnola (RSP10977)
  10. 0.160 Carmagnola USO 31 (RSP11204)
  11. 0.198 Tisza (RSP11044)
  12. 0.200 Kompolti (SRR14708277)
  13. 0.203 Tisza (RSP11045)
  14. 0.206 CS (RSP11208)
  15. 0.207 Chamaeleon (SRR14708197)
  16. 0.211 VIR 37 - Novgorod-Seversky - cv (SRR14708234)
  17. 0.211 C-930 lot 211005 (RSP12603)
  18. 0.215 Santhica27 (RSP11047)
  19. 0.215 Uniko B (SRR14708278)
  20. 0.215 Santhica27 (RSP10056)

Most genetically distant strains (All Samples)

0 0.108 0.217 0.325 0.433
closely related moderately related distantly related
  1. 0.424 Cherry Blossom (RSP11318)
  2. 0.423 Cherry Blossom (RSP11312)
  3. 0.421 Cherry Blossom (RSP11323)
  4. 0.416 BagSeed (RSP12627)
  5. 0.414 Unknown--Cherry Wine---001- (RSP11268)
  6. 0.414 Cherry Blossom (RSP11311)
  7. 0.412 Cherry Blossom (RSP11328)
  8. 0.410 Cherry Blossom (RSP11300)
  9. 0.409 Cherry Blossom (RSP11308)
  10. 0.407 Cherry Blossom (RSP11298)
  11. 0.405 Cherry Blossom (RSP11334)
  12. 0.405 Cherry Blossom (RSP11301)
  13. 0.405 Cherry Blossom (RSP11335)
  14. 0.404 Escape Velocity (RSP11165)
  15. 0.402 Chem 91 (RSP11185)
  16. 0.402 JL Cross 14 (RSP11515)
  17. 0.399 Northern Lights (RSP11501)
  18. 0.397 Cherry Blossom (RSP11332)
  19. 0.396 Queen Dream (RSP11278)
  20. 0.395 Goin Bananas (RSP12509)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448780
Overlapping SNPs:
47
Concordance:
30

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495209
Overlapping SNPs:
2
Concordance:
2

Blockchain Registration Information

Transaction ID
0e5427a505965ee32309dca420eb8965a1c8f0ad6ab77f7bde888518fef077fc
Stamping Certificate
Download PDF (862.0 KB)
SHASUM Hash
73fd908c7b1cd24db89166c71ec658598f6cca98806a8fd9c6ca4ca74ae7b00a
QR code for RSP10978

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