Carmagnola

RSP 10978

Grower: John McKay-Colorado State University

General Information

Sample Name
Carm_3_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: 1.09%
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: 0.0519
male female RSP10978

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-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.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
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.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. 0.004 Carmagnola (RSP10976)
  2. 0.004 Carmagnola (RSP10979)
  3. 0.008 Carmagnola (RSP11202)
  4. 0.125 Carmagnola (RSP10655)
  5. 0.130 Carmagnola (RSP10982)
  6. 0.139 Carmagnola (RSP11037)
  7. 0.139 Carmagnola (RSP11039)
  8. 0.145 Carmagnola (RSP10980)
  9. 0.146 Carmagnola (RSP10977)
  10. 0.150 Carmagnola USO 31 (RSP11204)
  11. 0.197 Tisza (RSP11045)
  12. 0.199 Tisza (RSP11044)
  13. 0.204 CS (RSP11208)
  14. 0.210 Tisza (RSP10659)
  15. 0.217 Santhica 27 (RSP10665)
  16. 0.218 Santhica27 (RSP10056)
  17. 0.219 Fedora 17 (RSP10661)
  18. 0.219 Santhica27 (RSP11046)
  19. 0.219 Feral (RSP10890)
  20. 0.220 Diana (RSP10235)

Nearest genetic relatives (Base Tree)

0 0.083 0.167 0.250 0.333
clone distance sibling distance more distant
  1. 0.003 Carmagnola (RSP10979)
  2. 0.142 Carmagnola (RSP11037)
  3. 0.194 Tisza (RSP11044)
  4. 0.218 Santhica27 (RSP11047)
  5. 0.223 Tygra (RSP10667)
  6. 0.225 Tisza (RSP10659)
  7. 0.226 Fedora 17 (RSP10661)
  8. 0.227 Ivory (RSP10668)
  9. 0.229 Monoica (RSP10241)
  10. 0.230 Futura 75 (RSP10664)
  11. 0.230 Feral (RSP10890)
  12. 0.230 Lovrin (RSP10658)
  13. 0.249 Kyrgyz Gold (RSP11054)
  14. 0.252 USO 31 (RSP10981)
  15. 0.252 KYRG-11 (RSP11051)
  16. 0.278 Jiangji (RSP10653)
  17. 0.302 Kimbo Slice (RSP10997)
  18. 0.303 Recon (RSP10755)
  19. 0.307 Hermaphrodite ResearchSample2 (RSP11050)
  20. 0.310 Durban Poison (RSP11014)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.448 Cherry Blossom (RSP11318)
  2. 0.441 Cherry Blossom (RSP11323)
  3. 0.438 Unknown- Cherry Wine - 001 (RSP11268)
  4. 0.435 Cherry Blossom (RSP11312)
  5. 0.434 Cherry Blossom (RSP11311)
  6. 0.431 Cherry Blossom (RSP11300)
  7. 0.418 Cherry Blossom (RSP11301)
  8. 0.417 Cherry Blossom (RSP11334)
  9. 0.416 Cherry Blossom (RSP11308)
  10. 0.415 Cherry Blossom (RSP11298)
  11. 0.415 Cherry Blossom (RSP11335)
  12. 0.413 Cherry Blossom (RSP11319)
  13. 0.409 Cherry Blossom (RSP11321)
  14. 0.409 Cherry Blossom (RSP11328)
  15. 0.407 Cherry Blossom (RSP11325)
  16. 0.407 Unknown- Cherry Wine - 002 (RSP11269)
  17. 0.407 Cherry Blossom (RSP11332)
  18. 0.404 Cherry Blossom (RSP11331)
  19. 0.404 Avidekel (RSP10938)
  20. 0.402 Unknown- Cherry Wine - 003 (RSP11270)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.396 Cbot-2019-005 (RSP11133)
  2. 0.370 Kush Hemp E1 (RSP11128)
  3. 0.369 Cbot-2019-001 (RSP11129)
  4. 0.367 RKM-2018-002 (RSP11093)
  5. 0.367 RKM-2018-018 (RSP11110)
  6. 0.360 RKM-2018-028 (RSP11120)
  7. 0.358 Cherry (RSP11143)
  8. 0.356 Skunk 18 (RSP11038)
  9. 0.354 RKM-2018-022 (RSP11114)
  10. 0.354 RKM-2018-023 (RSP11115)
  11. 0.353 Cbot-2019-004 (RSP11132)
  12. 0.351 Cherry (RSP11142)
  13. 0.348 RKM-2018-003 (RSP11094)
  14. 0.348 UP Sunrise (RSP10989)
  15. 0.346 Blueberry Cheesecake (RSP10672)
  16. 0.346 JL yellow (RSP11075)
  17. 0.345 RKM-2018-032 (RSP11124)
  18. 0.345 RKM-2018-005 (RSP11096)
  19. 0.345 Golden Goat 2 (RSP10991)
  20. 0.342 Liberty Haze (RSP11000)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448780
Overlapping SNPs:
47
Concordance:
30

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495209
Overlapping SNPs:
2
Concordance:
2

Blockchain Registration Information

Transaction ID
0e5427a505965ee32309dca420eb8965a1c8f0ad6ab77f7bde888518fef077fc
Stamping Certificate
Download PDF (862.0 KB)
SHASUM Hash
73fd908c7b1cd24db89166c71ec658598f6cca98806a8fd9c6ca4ca74ae7b00a
QR code for RSP10978

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