Carmagnola

RSP 11039

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 III

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: 1.11%
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: 0.0467
male female RSP11039

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-2b

UniProt

c.1117A>G p.Ile373Val missense variant moderate contig700 1950521

IGV: Start, Jump

T/C
NGS:
0.807
C90:
0.981
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
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 0.058 0.117 0.175 0.233
clone distance sibling distance more distant
  1. 0.003 Carmagnola (RSP10980)
  2. 0.004 Carmagnola (RSP11037)
  3. 0.005 Carmagnola (RSP10977)
  4. 0.006 Carmagnola (RSP10982)
  5. 0.134 Carmagnola (RSP10655)
  6. 0.142 Carmagnola (RSP10976)
  7. 0.145 Carmagnola (RSP10978)
  8. 0.145 Carmagnola (RSP10979)
  9. 0.155 Carmagnola (RSP11202)
  10. 0.191 CS (RSP11208)
  11. 0.207 Tisza (RSP11044)
  12. 0.210 VIR 37 - Novgorod-Seversky - cv (SRR14708234)
  13. 0.213 Carmagnola USO 31 (RSP11204)
  14. 0.213 Santhica27 (RSP10056)
  15. 0.218 Kompolti (SRR14708277)
  16. 0.221 Santhica 27 (RSP10665)
  17. 0.222 VIR 483 (SRR14708238)
  18. 0.222 Lovrin (RSP10658)
  19. 0.223 Tisza (RSP11045)
  20. 0.223 Ivory (RSP10668)

Nearest genetic relatives (Base Tree)

0 0.083 0.167 0.250 0.333
clone distance sibling distance more distant
  1. 0.002 Carmagnola (RSP11037)
  2. 0.155 Carmagnola (RSP10979)
  3. 0.216 Tisza (RSP11044)
  4. 0.218 Feral (RSP10890)
  5. 0.226 Lovrin (RSP10658)
  6. 0.230 Tisza (RSP10659)
  7. 0.233 Santhica27 (RSP11047)
  8. 0.237 Ivory (RSP10668)
  9. 0.238 Futura 75 (RSP10664)
  10. 0.240 KYRG-11 (RSP11051)
  11. 0.241 Fedora 17 (RSP10661)
  12. 0.244 Monoica (RSP10241)
  13. 0.249 Tygra (RSP10667)
  14. 0.251 USO 31 (RSP10981)
  15. 0.265 Kyrgyz Gold (RSP11054)
  16. 0.289 Jiangji (RSP10653)
  17. 0.295 Kimbo Slice (RSP10997)
  18. 0.313 Recon (RSP10755)
  19. 0.322 Blueberry Cheesecake (RSP10684)
  20. 0.322 Liberty Haze (RSP11000)

Most genetically distant strains (All Samples)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.425 Cherry Blossom (RSP11312)
  2. 0.425 Chem 91 (RSP11185)
  3. 0.422 Cherry Blossom (RSP11328)
  4. 0.418 Cherry Blossom (RSP11298)
  5. 0.417 Cherry Blossom (RSP11334)
  6. 0.417 Cherry Blossom (RSP11300)
  7. 0.412 Queen Dream CBG (RSP11293)
  8. 0.411 Cherry Blossom (RSP11311)
  9. 0.410 Escape Velocity (RSP11165)
  10. 0.409 BagSeed (RSP12627)
  11. 0.408 Cherry Blossom (RSP11323)
  12. 0.404 Glueberry OG (RSP11222)
  13. 0.404 Cherry Blossom (RSP11318)
  14. 0.403 Super Sour Diesel (RSP11191)
  15. 0.402 JL Tent 4 (RSP11491)
  16. 0.402 Cherry Blossom (RSP11301)
  17. 0.402 Skunk#18 (RSP11038)
  18. 0.402 RKM-2018-002 (RSP11093)
  19. 0.402 Cherry Blossom (RSP11309)
  20. 0.401 New York City Deisel (RSP11225)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.395 Cbot-2019-005 (RSP11133)
  2. 0.395 Skunk#18 (RSP11038)
  3. 0.383 RKM-2018-002 (RSP11093)
  4. 0.374 RKM-2018-022 (RSP11114)
  5. 0.374 RKM-2018-026 (RSP11118)
  6. 0.372 RKM-2018-004 (RSP11096)
  7. 0.372 Kush Hemp E1 (RSP11128)
  8. 0.371 RKM-2018-028 (RSP11120)
  9. 0.367 JL yellow (RSP11075)
  10. 0.367 RKM-2018-023 (RSP11115)
  11. 0.366 RKM-2018-027 (RSP11119)
  12. 0.365 RKM-2018-032 (RSP11124)
  13. 0.365 Gold Cracker (RSP11048)
  14. 0.359 Cbot-2019-001 (RSP11129)
  15. 0.357 The Gift (RSP10988)
  16. 0.357 RKM-2018-033 (RSP11125)
  17. 0.356 Cherry (RSP11142)
  18. 0.355 RKM-2018-020 (RSP11112)
  19. 0.354 Skywalker OG (RSP10837)
  20. 0.354 RKM-2018-018 (RSP11110)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448780
Overlapping SNPs:
42
Concordance:
30

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495166
Overlapping SNPs:
2
Concordance:
2

Blockchain Registration Information

Transaction ID
0e5a4cafb49fd5c8c222a7f021f897f3f64816309f8c21d536c78208d6806565
Stamping Certificate
Download PDF (865.8 KB)
SHASUM Hash
d252dea9d5075793e490595a13b92ed63d342803b3ab3f84bebef8ebafb03396
QR code for RSP11039

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