Carmagnola

RSP 10982

Grower: John McKay-Colorado State University

General Information

Sample Name
Carm_24_2_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: 1.03%
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 RSP10982

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.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. 0.004 Carmagnola (RSP10980)
  3. 0.005 Carmagnola (RSP10977)
  4. 0.006 Carmagnola (RSP11039)
  5. 0.130 Carmagnola (RSP10978)
  6. 0.134 Carmagnola (RSP10976)
  7. 0.148 Carmagnola (RSP10979)
  8. 0.153 Carmagnola (RSP10655)
  9. 0.162 Carmagnola (RSP11202)
  10. 0.199 Carmagnola USO 31 (RSP11204)
  11. 0.201 CS (RSP11208)
  12. 0.201 Lovrin (RSP10658)
  13. 0.203 Futura 75 (RSP10664)
  14. 0.203 Tisza (RSP10659)
  15. 0.208 Tisza (RSP11045)
  16. 0.211 Santhica 27 (RSP10665)
  17. 0.212 Tisza (RSP11044)
  18. 0.213 Santhica27 (RSP11046)
  19. 0.214 Fedora 17 (RSP10661)
  20. 0.215 USO 31 (RSP10983)

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. 0.158 Carmagnola (RSP10979)
  3. 0.202 Tisza (RSP10659)
  4. 0.203 Lovrin (RSP10658)
  5. 0.205 Futura 75 (RSP10664)
  6. 0.208 Tisza (RSP11044)
  7. 0.213 Santhica27 (RSP11047)
  8. 0.213 Tygra (RSP10667)
  9. 0.221 Ivory (RSP10668)
  10. 0.223 Fedora 17 (RSP10661)
  11. 0.224 KYRG-11 (RSP11051)
  12. 0.230 USO 31 (RSP10981)
  13. 0.231 Feral (RSP10890)
  14. 0.238 Monoica (RSP10241)
  15. 0.240 Jiangji (RSP10653)
  16. 0.248 Kyrgyz Gold (RSP11054)
  17. 0.266 Kimbo Slice (RSP10997)
  18. 0.288 Recon (RSP10755)
  19. 0.300 RKM-2018-029 (RSP11121)
  20. 0.302 Liberty Haze (RSP11000)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.445 Cherry Blossom (RSP11323)
  2. 0.429 Cherry Blossom (RSP11312)
  3. 0.427 Cherry Blossom (RSP11300)
  4. 0.425 Cherry Blossom (RSP11318)
  5. 0.423 Unknown- Cherry Wine - 001 (RSP11268)
  6. 0.422 Unknown- Cherry Wine - 002 (RSP11269)
  7. 0.420 Cherry Blossom (RSP11298)
  8. 0.419 Cherry Blossom (RSP11328)
  9. 0.415 Cherry Blossom (RSP11311)
  10. 0.414 Unknown- Cherry Wine - 003 (RSP11270)
  11. 0.408 Cherry Blossom (RSP11309)
  12. 0.407 Cherry Blossom (RSP11321)
  13. 0.405 Cherry Blossom (RSP11301)
  14. 0.402 Cherry Blossom (RSP11319)
  15. 0.399 Cherry Blossom (RSP11334)
  16. 0.399 Avidekel (RSP10938)
  17. 0.394 Cherry Blossom CBG (RSP11303)
  18. 0.393 Cherry Blossom (RSP11331)
  19. 0.393 Cherry Blossom (RSP11316)
  20. 0.393 Cherry Blossom (RSP11332)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.385 Cbot-2019-005 (RSP11133)
  2. 0.363 Skunk 18 (RSP11038)
  3. 0.361 Kush Hemp E1 (RSP11128)
  4. 0.358 RKM-2018-028 (RSP11120)
  5. 0.357 RKM-2018-018 (RSP11110)
  6. 0.356 RKM-2018-002 (RSP11093)
  7. 0.355 Cbot-2019-001 (RSP11129)
  8. 0.354 Cherry (RSP11143)
  9. 0.353 RKM-2018-023 (RSP11115)
  10. 0.351 Cbot-2019-004 (RSP11132)
  11. 0.350 JL yellow (RSP11075)
  12. 0.344 Blueberry Cheesecake (RSP10672)
  13. 0.339 Gold Cracker (RSP11048)
  14. 0.338 RKM-2018-022 (RSP11114)
  15. 0.335 RKM-2018-005 (RSP11096)
  16. 0.334 RKM-2018-032 (RSP11124)
  17. 0.333 Cherry (RSP11142)
  18. 0.332 Sour Raspberry (RSP10551)
  19. 0.332 UP Sunrise (RSP10989)
  20. 0.329 RKM-2018-003 (RSP11094)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448780
Overlapping SNPs:
44
Concordance:
30

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495248
Overlapping SNPs:
4
Concordance:
4

Blockchain Registration Information

Transaction ID
50ebe671a671b0c70981f3f38ae74cb61a18f8458567a461a73c558f7357b898
Stamping Certificate
Download PDF (858.1 KB)
SHASUM Hash
b611936d1d87a7eddee5c801d4b09d16b6c603ff76413c6da52fa3aa70c4cac9
QR code for RSP10982

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