Carmagnola

RSP 10979

Grower: John McKay-Colorado State University

General Information

Sample Name
Carm_3_3_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: 1.13%
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: 0.0516
male female RSP10979

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
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.948T>G p.Asp316Glu missense variant moderate contig700 1950690

IGV: Start, Jump

A/C
NGS:
0.456
C90:
0.000
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
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
clone distance sibling distance more distant
  1. 0.003 Carmagnola (RSP10978)
  2. 0.005 Carmagnola (RSP10976)
  3. 0.006 Carmagnola (RSP11202)
  4. 0.111 Carmagnola (RSP10655)
  5. 0.136 Carmagnola (RSP10982)
  6. 0.145 Carmagnola (RSP11039)
  7. 0.151 Carmagnola (RSP10977)
  8. 0.152 Carmagnola (RSP10980)
  9. 0.152 Carmagnola (RSP11037)
  10. 0.154 Carmagnola USO 31 (RSP11204)
  11. 0.192 Tisza (RSP11044)
  12. 0.196 CS (RSP11208)
  13. 0.200 Tisza (RSP11045)
  14. 0.204 Kompolti (SRR14708277)
  15. 0.210 Tisza (RSP10659)
  16. 0.211 VIR 483 (SRR14708238)
  17. 0.211 Santhica27 (RSP10056)
  18. 0.214 C-930 lot 211005 (RSP12603)
  19. 0.214 Futura 75 (RSP10664)
  20. 0.214 Uniko B (SRR14708278)

Nearest genetic relatives (Base Tree)

0 0.083 0.167 0.250 0.333
clone distance sibling distance more distant
  1. 0.155 Carmagnola (RSP11037)
  2. 0.201 Tisza (RSP11044)
  3. 0.227 Tisza (RSP10659)
  4. 0.230 Fedora 17 (RSP10661)
  5. 0.233 Futura 75 (RSP10664)
  6. 0.235 Santhica27 (RSP11047)
  7. 0.235 Monoica (RSP10241)
  8. 0.236 Feral (RSP10890)
  9. 0.240 Ivory (RSP10668)
  10. 0.243 Lovrin (RSP10658)
  11. 0.249 Tygra (RSP10667)
  12. 0.257 Kyrgyz Gold (RSP11054)
  13. 0.260 KYRG-11 (RSP11051)
  14. 0.279 USO 31 (RSP10981)
  15. 0.286 Jiangji (RSP10653)
  16. 0.299 Blueberry Cheesecake (RSP10684)
  17. 0.302 Liberty Haze (RSP11000)
  18. 0.309 Recon (RSP10755)
  19. 0.313 Kimbo Slice (RSP10997)
  20. 0.314 Durban Poison (RSP11014)

Most genetically distant strains (All Samples)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.428 Cherry Blossom (RSP11312)
  2. 0.426 Cherry Blossom (RSP11318)
  3. 0.426 Cherry Blossom (RSP11323)
  4. 0.421 Chem 91 (RSP11185)
  5. 0.419 BagSeed (RSP12627)
  6. 0.415 Cherry Blossom (RSP11300)
  7. 0.413 JL Cross 14 (RSP11515)
  8. 0.412 Cherry Blossom (RSP11311)
  9. 0.412 Cherry Blossom (RSP11308)
  10. 0.411 Cherry Blossom (RSP11298)
  11. 0.409 Cherry Blossom (RSP11335)
  12. 0.409 Cherry Blossom (RSP11301)
  13. 0.407 Cherry Blossom (RSP11328)
  14. 0.405 Escape Velocity (RSP11165)
  15. 0.402 Unknown--Cherry Wine---001- (RSP11268)
  16. 0.398 Fatso (RSP11741)
  17. 0.397 Northern Lights (RSP11501)
  18. 0.396 GMO x Garlic Breath (RSP12507)
  19. 0.396 RKM-2018-002 (RSP11093)
  20. 0.395 Cherry Blossom (RSP11334)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.389 Cbot-2019-005 (RSP11133)
  2. 0.387 RKM-2018-002 (RSP11093)
  3. 0.378 Kush Hemp E1 (RSP11128)
  4. 0.377 RKM-2018-023 (RSP11115)
  5. 0.376 RKM-2018-018 (RSP11110)
  6. 0.373 Cherry (RSP11142)
  7. 0.370 RKM-2018-003 (RSP11094)
  8. 0.369 RKM-2018-022 (RSP11114)
  9. 0.369 Cbot-2019-001 (RSP11129)
  10. 0.367 The Gift (RSP10988)
  11. 0.365 RKM-2018-028 (RSP11120)
  12. 0.365 JL yellow (RSP11075)
  13. 0.363 RKM-2018-004 (RSP11096)
  14. 0.363 Skywalker OG (RSP10837)
  15. 0.362 Pie Hoe (RSP11073)
  16. 0.362 Skunk#18 (RSP11038)
  17. 0.360 RKM-2018-034 (RSP11126)
  18. 0.359 Gold Cracker (RSP11048)
  19. 0.358 RKM-2018-032 (RSP11124)
  20. 0.358 Italian Kiss (RSP11034)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448780
Overlapping SNPs:
47
Concordance:
31

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495248
Overlapping SNPs:
2
Concordance:
2

Blockchain Registration Information

Transaction ID
dda79addd2ae73a92d8a12b5ded4710641f86c50007f1112c5bb62e7ef192f9c
Stamping Certificate
Download PDF (842.1 KB)
SHASUM Hash
ebd8f5785997922c6477d069f67013b0198880a9f03c1000d7a300f97bfba30d
QR code for RSP10979

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