Carmagnola

RSP 11037

Grower: John McKay-Colorado State University

General Information

Sample Name
Carm_24_2_CSU
Accession Date
November 19, 2017
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 I

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: 1.02%
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: 0.0509
male female RSP11037

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-4a

UniProt

c.493G>A p.Gly165Ser missense variant moderate contig700 1937904

IGV: Start, Jump

G/A
NGS:
0.103
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-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
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.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

Nearest genetic relatives (All Samples)

0 0.058 0.117 0.175 0.233
clone distance sibling distance more distant
  1. 0.002 Carmagnola (RSP10980)
  2. 0.002 Carmagnola (RSP10977)
  3. 0.002 Carmagnola (RSP10982)
  4. 0.004 Carmagnola (RSP11039)
  5. 0.140 Carmagnola (RSP10655)
  6. 0.145 Carmagnola (RSP10978)
  7. 0.149 Carmagnola (RSP10976)
  8. 0.152 Carmagnola (RSP10979)
  9. 0.159 Carmagnola (RSP11202)
  10. 0.185 CS (RSP11208)
  11. 0.211 Santhica27 (RSP10056)
  12. 0.218 VIR 37 - Novgorod-Seversky - cv (SRR14708234)
  13. 0.219 Carmagnola USO 31 (RSP11204)
  14. 0.223 Kompolti (SRR14708277)
  15. 0.223 Tisza (RSP11044)
  16. 0.223 Santhica27 (RSP11046)
  17. 0.224 Ivory (RSP10668)
  18. 0.224 Santhica27 (RSP11047)
  19. 0.225 VIR 201 (SRR14708232)
  20. 0.227 Carmagnola (SRR14708200)

Nearest genetic relatives (Base Tree)

0 0.092 0.183 0.275 0.367
clone distance sibling distance more distant
  1. 0.155 Carmagnola (RSP10979)
  2. 0.217 Santhica27 (RSP11047)
  3. 0.220 Tisza (RSP11044)
  4. 0.228 Tisza (RSP10659)
  5. 0.230 Lovrin (RSP10658)
  6. 0.231 Feral (RSP10890)
  7. 0.233 Fedora 17 (RSP10661)
  8. 0.237 Tygra (RSP10667)
  9. 0.238 Ivory (RSP10668)
  10. 0.239 Futura 75 (RSP10664)
  11. 0.242 Monoica (RSP10241)
  12. 0.245 USO 31 (RSP10981)
  13. 0.254 KYRG-11 (RSP11051)
  14. 0.263 Kyrgyz Gold (RSP11054)
  15. 0.292 Jiangji (RSP10653)
  16. 0.314 Kimbo Slice (RSP10997)
  17. 0.328 Recon (RSP10755)
  18. 0.334 Liberty Haze (RSP11000)
  19. 0.340 UP Sunrise (RSP10989)
  20. 0.342 RKM-2018-029 (RSP11121)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.451 Cherry Blossom (RSP11312)
  2. 0.445 Cherry Blossom (RSP11300)
  3. 0.441 Cherry Blossom (RSP11298)
  4. 0.433 Cherry Blossom (RSP11328)
  5. 0.426 Skunk#18 (RSP11038)
  6. 0.424 Northern Skunk (RSP11456)
  7. 0.424 Queen Dream CBG (RSP11293)
  8. 0.423 JL Cross 14 (RSP11515)
  9. 0.423 Cherry Blossom (RSP11309)
  10. 0.422 Chem 91 (RSP11185)
  11. 0.422 Cherry Blossom (RSP11311)
  12. 0.421 Cherry Blossom (RSP11301)
  13. 0.421 BagSeed (RSP12627)
  14. 0.421 Queen Dream (RSP11278)
  15. 0.420 Cherry Blossom (RSP11323)
  16. 0.418 Escape Velocity (RSP11165)
  17. 0.418 RKM-2018-002 (RSP11093)
  18. 0.418 New York City Deisel (RSP11225)
  19. 0.417 Cherry Blossom (RSP11334)
  20. 0.417 Glueberry OG (RSP11222)

Most genetically distant strains (Base Tree)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.417 Skunk#18 (RSP11038)
  2. 0.402 RKM-2018-002 (RSP11093)
  3. 0.399 Cbot-2019-005 (RSP11133)
  4. 0.391 RKM-2018-032 (RSP11124)
  5. 0.388 RKM-2018-026 (RSP11118)
  6. 0.386 Kush Hemp E1 (RSP11128)
  7. 0.386 RKM-2018-028 (RSP11120)
  8. 0.385 RKM-2018-027 (RSP11119)
  9. 0.384 JL yellow (RSP11075)
  10. 0.383 RKM-2018-022 (RSP11114)
  11. 0.382 RKM-2018-020 (RSP11112)
  12. 0.381 RKM-2018-023 (RSP11115)
  13. 0.380 RKM-2018-004 (RSP11096)
  14. 0.378 RKM-2018-018 (RSP11110)
  15. 0.378 Cherry (RSP11142)
  16. 0.376 Cbot-2019-001 (RSP11129)
  17. 0.376 RKM-2018-033 (RSP11125)
  18. 0.374 Skywalker OG (RSP10837)
  19. 0.374 Gold Cracker (RSP11048)
  20. 0.373 Pie Hoe (RSP11073)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448780
Overlapping SNPs:
52
Concordance:
37

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495248
Overlapping SNPs:
4
Concordance:
4

Blockchain Registration Information

Transaction ID
cffda855b9399efedba49292b8aaf22ed06b64b0119d6c0aa9f45ef755d9476f
Stamping Certificate
Download PDF (858.1 KB)
SHASUM Hash
cfa486a7a81f7885628f3129cd26a3d3776ce1b7180c51001185f007bef34575
QR code for RSP11037

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