Carmagnola

RSP 10976

Grower: John McKay-Colorado State University

General Information

Sample Name
Carm_3_1_CSU
Accession Date
July 16, 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: 1.16%
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: 0.0501
male female RSP10976

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-2a

UniProt

c.31A>T p.Thr11Ser missense variant moderate contig700 1945603

IGV: Start, Jump

T/A
NGS:
0.763
C90:
0.876
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.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
clone distance sibling distance more distant
  1. 0.003 Carmagnola (RSP10978)
  2. 0.005 Carmagnola (RSP10979)
  3. 0.009 Carmagnola (RSP11202)
  4. 0.106 Carmagnola (RSP10655)
  5. 0.129 Carmagnola (RSP10982)
  6. 0.142 Carmagnola (RSP11039)
  7. 0.145 Carmagnola (RSP10980)
  8. 0.149 Carmagnola (RSP11037)
  9. 0.152 Carmagnola (RSP10977)
  10. 0.156 Carmagnola USO 31 (RSP11204)
  11. 0.202 C-930 lot 211005 (RSP12603)
  12. 0.205 Tisza (RSP11044)
  13. 0.210 VIR 469 (SRR14708243)
  14. 0.210 Chamaeleon (SRR14708197)
  15. 0.210 Kompolti (SRR14708277)
  16. 0.211 Santhica27 (RSP10056)
  17. 0.211 VIR 37 - Novgorod-Seversky - cv (SRR14708234)
  18. 0.214 Tisza (RSP11045)
  19. 0.214 CS (RSP11208)
  20. 0.215 VIR 483 (SRR14708238)

Nearest genetic relatives (Base Tree)

0 0.083 0.167 0.250 0.333
clone distance sibling distance more distant
  1. 0.006 Carmagnola (RSP10979)
  2. 0.153 Carmagnola (RSP11037)
  3. 0.215 Tisza (RSP11044)
  4. 0.233 Monoica (RSP10241)
  5. 0.234 Ivory (RSP10668)
  6. 0.235 Santhica27 (RSP11047)
  7. 0.238 Feral (RSP10890)
  8. 0.240 Tisza (RSP10659)
  9. 0.246 Tygra (RSP10667)
  10. 0.248 Fedora 17 (RSP10661)
  11. 0.248 Futura 75 (RSP10664)
  12. 0.248 Lovrin (RSP10658)
  13. 0.266 Kyrgyz Gold (RSP11054)
  14. 0.281 USO 31 (RSP10981)
  15. 0.283 KYRG-11 (RSP11051)
  16. 0.284 Jiangji (RSP10653)
  17. 0.295 Blueberry Cheesecake (RSP10684)
  18. 0.300 Durban Poison (RSP11014)
  19. 0.312 Hermaphrodite ResearchSample2 (RSP11050)
  20. 0.314 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. 0.432 Chem 91 (RSP11185)
  2. 0.411 Cherry Blossom (RSP11318)
  3. 0.407 Cherry Blossom (RSP11300)
  4. 0.406 Escape Velocity (RSP11165)
  5. 0.405 Cherry Blossom (RSP11308)
  6. 0.404 BagSeed (RSP12627)
  7. 0.403 Northern Lights (RSP11501)
  8. 0.402 Cherry Blossom (RSP11312)
  9. 0.399 Cherry Blossom (RSP11335)
  10. 0.399 Cherry Blossom (RSP11328)
  11. 0.399 Cherry Blossom (RSP11298)
  12. 0.398 GMO x Garlic Breath (RSP12507)
  13. 0.398 GG4 (RSP11978)
  14. 0.396 Cherry Blossom (RSP11301)
  15. 0.396 CBG #30 (RSP11447)
  16. 0.396 Cherry Blossom (RSP11323)
  17. 0.396 Queen Dream (RSP11278)
  18. 0.395 JL Cross 14 (RSP11515)
  19. 0.395 Cherry Blossom (RSP11311)
  20. 0.393 Fatso (RSP11741)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.384 RKM-2018-002 (RSP11093)
  2. 0.375 Cherry (RSP11142)
  3. 0.373 Kush Hemp E1 (RSP11128)
  4. 0.373 RKM-2018-023 (RSP11115)
  5. 0.373 Cbot-2019-005 (RSP11133)
  6. 0.362 RKM-2018-028 (RSP11120)
  7. 0.359 RKM-2018-026 (RSP11118)
  8. 0.358 JL yellow (RSP11075)
  9. 0.357 RKM-2018-022 (RSP11114)
  10. 0.354 RKM-2018-018 (RSP11110)
  11. 0.354 Cbot-2019-001 (RSP11129)
  12. 0.353 Blue Dream (RSP11033)
  13. 0.353 RKM-2018-032 (RSP11124)
  14. 0.353 Skywalker OG (RSP10837)
  15. 0.352 Italian Kiss (RSP11034)
  16. 0.352 RKM-2018-003 (RSP11094)
  17. 0.352 RKM-2018-004 (RSP11096)
  18. 0.351 The Gift (RSP10988)
  19. 0.348 Skunk#18 (RSP11038)
  20. 0.347 RKM-2018-031 (RSP11123)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448780
Overlapping SNPs:
43
Concordance:
28

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495248
Overlapping SNPs:
3
Concordance:
3

Blockchain Registration Information

Transaction ID
383f0c866999546872edb65563d8298d5f52bb50763413ff9c9c359466a7688d
Stamping Certificate
Download PDF (873.5 KB)
SHASUM Hash
fe2b64ed3bd5761c8ac29eda8187a4e30a5d31ffaa31cc527eeacebf1947fb3b
QR code for RSP10976

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