Carmagnola

RSP 10977

Grower: John McKay-Colorado State University

General Information

Sample Name
Carm_24_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: 1.03%
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: 0.0524
male female RSP10977

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
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 (RSP10980)
  3. 0.003 Carmagnola (RSP11039)
  4. 0.005 Carmagnola (RSP10982)
  5. 0.146 Carmagnola (RSP10978)
  6. 0.148 Carmagnola (RSP10976)
  7. 0.151 Carmagnola (RSP10979)
  8. 0.161 Carmagnola (RSP10655)
  9. 0.170 Carmagnola (RSP11202)
  10. 0.207 CS (RSP11208)
  11. 0.214 Futura 75 (RSP10664)
  12. 0.216 Santhica 27 (RSP10665)
  13. 0.217 Lovrin (RSP10658)
  14. 0.219 Santhica27 (RSP11046)
  15. 0.220 Carmagnola USO 31 (RSP11204)
  16. 0.220 Diana (RSP10235)
  17. 0.221 Fedora 17 (RSP10661)
  18. 0.221 USO 31 (RSP10983)
  19. 0.222 Santhica27 (RSP10056)
  20. 0.222 Santhica27 (RSP11047)

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. 0.157 Carmagnola (RSP10979)
  3. 0.214 Futura 75 (RSP10664)
  4. 0.216 Santhica27 (RSP11047)
  5. 0.220 Lovrin (RSP10658)
  6. 0.222 Tisza (RSP11044)
  7. 0.225 Tygra (RSP10667)
  8. 0.229 Tisza (RSP10659)
  9. 0.229 Fedora 17 (RSP10661)
  10. 0.231 USO 31 (RSP10981)
  11. 0.239 Feral (RSP10890)
  12. 0.242 Ivory (RSP10668)
  13. 0.246 Monoica (RSP10241)
  14. 0.251 KYRG-11 (RSP11051)
  15. 0.258 Kyrgyz Gold (RSP11054)
  16. 0.266 Jiangji (RSP10653)
  17. 0.280 Kimbo Slice (RSP10997)
  18. 0.299 Recon (RSP10755)
  19. 0.319 RKM-2018-029 (RSP11121)
  20. 0.322 Hermaphrodite ResearchSample2 (RSP11050)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.446 Cherry Blossom (RSP11323)
  2. 0.444 Cherry Blossom (RSP11312)
  3. 0.443 Cherry Blossom (RSP11318)
  4. 0.436 Cherry Blossom (RSP11300)
  5. 0.426 Cherry Blossom (RSP11328)
  6. 0.421 Unknown- Cherry Wine - 002 (RSP11269)
  7. 0.421 Unknown- Cherry Wine - 001 (RSP11268)
  8. 0.420 Cherry Blossom (RSP11311)
  9. 0.418 Cherry Blossom (RSP11331)
  10. 0.416 Avidekel (RSP10938)
  11. 0.415 Cherry Blossom (RSP11298)
  12. 0.415 Cherry Blossom (RSP11334)
  13. 0.414 Cherry Blossom (RSP11321)
  14. 0.412 Cherry Blossom (RSP11301)
  15. 0.412 Cherry Blossom (RSP11316)
  16. 0.409 Cherry Blossom (RSP11319)
  17. 0.409 Cherry Blossom (RSP11310)
  18. 0.408 AVIDEKEL 2 0 (RSP11174)
  19. 0.406 Unknown- Cherry Wine - 003 (RSP11270)
  20. 0.406 Cherry Blossom (RSP11309)

Most genetically distant strains (Base Tree)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.403 Cbot-2019-005 (RSP11133)
  2. 0.388 Skunk 18 (RSP11038)
  3. 0.387 Kush Hemp E1 (RSP11128)
  4. 0.379 RKM-2018-002 (RSP11093)
  5. 0.376 RKM-2018-018 (RSP11110)
  6. 0.369 RKM-2018-028 (RSP11120)
  7. 0.369 Cbot-2019-004 (RSP11132)
  8. 0.366 Cbot-2019-001 (RSP11129)
  9. 0.363 JL yellow (RSP11075)
  10. 0.362 RKM-2018-023 (RSP11115)
  11. 0.360 Blueberry Cheesecake (RSP10672)
  12. 0.358 RKM-2018-022 (RSP11114)
  13. 0.355 Cherry (RSP11143)
  14. 0.354 RKM-2018-032 (RSP11124)
  15. 0.354 RKM-2018-005 (RSP11096)
  16. 0.354 UP Sunrise (RSP10989)
  17. 0.352 RKM-2018-020 (RSP11112)
  18. 0.349 Gold Cracker (RSP11048)
  19. 0.348 RKM-2018-033 (RSP11125)
  20. 0.348 RKM-2018-003 (RSP11094)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448780
Overlapping SNPs:
46
Concordance:
31

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495166
Overlapping SNPs:
2
Concordance:
2

Blockchain Registration Information

Transaction ID
5b14580ae1338b3def43914f9a20c5e94eaea1fd472a50e8fac95c90237de3a6
Stamping Certificate
Download PDF (859.2 KB)
SHASUM Hash
f6c4d0a2025c08ef2914d756352aabc2f7ec07a05e0c2cbf2884f8d7b01497a2
QR code for RSP10977

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