Carmagnola

RSP 10980

Grower: John McKay-Colorado State University

General Information

Sample Name
Carm_24_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: 1.01%
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 RSP10980

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
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

Nearest genetic relatives (All Samples)

0 0.058 0.117 0.175 0.233
clone distance sibling distance more distant
  1. 0.002 Carmagnola (RSP11037)
  2. 0.002 Carmagnola (RSP10982)
  3. 0.003 Carmagnola (RSP10977)
  4. 0.003 Carmagnola (RSP11039)
  5. 0.139 Carmagnola (RSP10655)
  6. 0.145 Carmagnola (RSP10976)
  7. 0.146 Carmagnola (RSP10978)
  8. 0.152 Carmagnola (RSP10979)
  9. 0.160 Carmagnola (RSP11202)
  10. 0.183 CS (RSP11208)
  11. 0.205 Santhica27 (RSP10056)
  12. 0.212 VIR 37 - Novgorod-Seversky - cv (SRR14708234)
  13. 0.219 Carmagnola USO 31 (RSP11204)
  14. 0.219 VIR 201 (SRR14708232)
  15. 0.221 Santhica27 (RSP11047)
  16. 0.224 Santhica27 (RSP11046)
  17. 0.225 Tisza (RSP11044)
  18. 0.226 Santhica 27 (RSP10665)
  19. 0.226 Kompolti (SRR14708277)
  20. 0.227 Ivory (RSP10668)

Nearest genetic relatives (Base Tree)

0 0.083 0.167 0.250 0.333
clone distance sibling distance more distant
  1. 0.003 Carmagnola (RSP11037)
  2. 0.159 Carmagnola (RSP10979)
  3. 0.224 Santhica27 (RSP11047)
  4. 0.227 Feral (RSP10890)
  5. 0.228 Fedora 17 (RSP10661)
  6. 0.229 Lovrin (RSP10658)
  7. 0.229 Tisza (RSP10659)
  8. 0.229 Tisza (RSP11044)
  9. 0.230 Futura 75 (RSP10664)
  10. 0.244 Tygra (RSP10667)
  11. 0.245 Monoica (RSP10241)
  12. 0.249 USO 31 (RSP10981)
  13. 0.249 Ivory (RSP10668)
  14. 0.252 KYRG-11 (RSP11051)
  15. 0.256 Kyrgyz Gold (RSP11054)
  16. 0.288 Jiangji (RSP10653)
  17. 0.305 Recon (RSP10755)
  18. 0.314 Kimbo Slice (RSP10997)
  19. 0.326 Liberty Haze (RSP11000)
  20. 0.328 Sour Raspberry (RSP10551)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.447 Cherry Blossom (RSP11312)
  2. 0.447 Cherry Blossom (RSP11298)
  3. 0.446 Cherry Blossom (RSP11328)
  4. 0.437 Cherry Blossom (RSP11323)
  5. 0.437 Chem 91 (RSP11185)
  6. 0.430 Cherry Blossom (RSP11309)
  7. 0.428 Cherry Blossom (RSP11300)
  8. 0.422 New York City Deisel (RSP11225)
  9. 0.420 RKM-2018-002 (RSP11093)
  10. 0.419 Super Sour Diesel (RSP11191)
  11. 0.418 Cherry Blossom (RSP11311)
  12. 0.418 Cherry Blossom (RSP11318)
  13. 0.418 Queen Dream CBG (RSP11293)
  14. 0.417 JL X NSPM1 30 (RSP11476)
  15. 0.417 Cherry Blossom (RSP11301)
  16. 0.416 Northern Skunk (RSP11456)
  17. 0.416 JL Tent 4 (RSP11491)
  18. 0.415 Cherry Blossom CBG (RSP11303)
  19. 0.415 Cherry Blossom (RSP11334)
  20. 0.414 JL Cross 14 (RSP11515)

Most genetically distant strains (Base Tree)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.402 RKM-2018-002 (RSP11093)
  2. 0.398 Skunk#18 (RSP11038)
  3. 0.393 Cbot-2019-005 (RSP11133)
  4. 0.382 JL yellow (RSP11075)
  5. 0.379 RKM-2018-026 (RSP11118)
  6. 0.377 RKM-2018-032 (RSP11124)
  7. 0.377 RKM-2018-004 (RSP11096)
  8. 0.376 Kush Hemp E1 (RSP11128)
  9. 0.373 Cbot-2019-001 (RSP11129)
  10. 0.372 RKM-2018-023 (RSP11115)
  11. 0.371 The Gift (RSP10988)
  12. 0.369 RKM-2018-033 (RSP11125)
  13. 0.369 Skywalker OG (RSP10837)
  14. 0.368 RKM-2018-027 (RSP11119)
  15. 0.367 RKM-2018-020 (RSP11112)
  16. 0.364 RKM-2018-028 (RSP11120)
  17. 0.364 RKM-2018-022 (RSP11114)
  18. 0.362 Cherry (RSP11142)
  19. 0.361 RKM-2018-018 (RSP11110)
  20. 0.360 Cherry (RSP11143)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448780
Overlapping SNPs:
49
Concordance:
34

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495248
Overlapping SNPs:
4
Concordance:
4

Blockchain Registration Information

Transaction ID
cc1c3534b46af787f9f34db17ac54601aa067eaca99be12867060c929adb34ca
Stamping Certificate
Download PDF (864.2 KB)
SHASUM Hash
2b0cb42b290f310c468e3883d331fe534a7da378dc269a20738a5013f8ecb983
QR code for RSP10980

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