Carmagnola

RSP 10976

Grower: John McKay-Colorado State University

General Information

Sample Name
Carm_3_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: 1.16%
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 RSP10976

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
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.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. 0.002 Carmagnola (RSP10979)
  2. 0.004 Carmagnola (RSP10978)
  3. 0.008 Carmagnola (RSP11202)
  4. 0.131 Carmagnola (RSP10655)
  5. 0.134 Carmagnola (RSP10982)
  6. 0.142 Carmagnola (RSP11039)
  7. 0.148 Carmagnola (RSP10977)
  8. 0.150 Carmagnola (RSP11037)
  9. 0.153 Carmagnola (RSP10980)
  10. 0.162 Carmagnola USO 31 (RSP11204)
  11. 0.205 CS (RSP11208)
  12. 0.206 Tisza (RSP11044)
  13. 0.207 Tisza (RSP11045)
  14. 0.211 Tygra (RSP10667)
  15. 0.216 Santhica 27 (RSP10665)
  16. 0.216 Ivory (RSP10668)
  17. 0.219 Diana (RSP10235)
  18. 0.219 Santhica27 (RSP11046)
  19. 0.221 Feral (RSP10890)
  20. 0.222 Santhica27 (RSP10056)

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. 0.154 Carmagnola (RSP11037)
  3. 0.206 Tisza (RSP11044)
  4. 0.213 Tygra (RSP10667)
  5. 0.219 Ivory (RSP10668)
  6. 0.226 Futura 75 (RSP10664)
  7. 0.226 Feral (RSP10890)
  8. 0.228 Monoica (RSP10241)
  9. 0.228 Fedora 17 (RSP10661)
  10. 0.232 Tisza (RSP10659)
  11. 0.234 Santhica27 (RSP11047)
  12. 0.238 Lovrin (RSP10658)
  13. 0.246 Kyrgyz Gold (RSP11054)
  14. 0.255 USO 31 (RSP10981)
  15. 0.259 KYRG-11 (RSP11051)
  16. 0.264 Jiangji (RSP10653)
  17. 0.295 Durban Poison (RSP11014)
  18. 0.301 RKM-2018-029 (RSP11121)
  19. 0.301 Blueberry Cheesecake (RSP10684)
  20. 0.303 Kimbo Slice (RSP10997)

Most genetically distant strains (All Samples)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.430 Cherry Blossom (RSP11318)
  2. 0.430 Cherry Blossom (RSP11323)
  3. 0.425 Cherry Blossom (RSP11311)
  4. 0.421 Cherry Blossom (RSP11334)
  5. 0.420 Cherry Blossom (RSP11308)
  6. 0.418 Cherry Blossom (RSP11335)
  7. 0.408 Cherry Blossom (RSP11300)
  8. 0.408 Cherry Blossom (RSP11312)
  9. 0.406 Cherry Blossom (RSP11301)
  10. 0.405 Unknown- Cherry Wine - 001 (RSP11268)
  11. 0.398 Cherry Blossom (RSP11298)
  12. 0.397 80E (RSP11213)
  13. 0.395 Cherry Blossom (RSP11332)
  14. 0.393 Cherry Blossom (RSP11321)
  15. 0.393 Cherry Blossom (RSP11333)
  16. 0.389 Cherry Blossom (RSP11319)
  17. 0.389 Queen Dream (RSP11278)
  18. 0.389 Cherry Blossom (RSP11328)
  19. 0.388 Cherry Blossom (RSP11324)
  20. 0.386 Cherry Blossom (RSP11331)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.383 Cbot-2019-005 (RSP11133)
  2. 0.372 Kush Hemp E1 (RSP11128)
  3. 0.361 Cbot-2019-001 (RSP11129)
  4. 0.357 RKM-2018-002 (RSP11093)
  5. 0.357 RKM-2018-018 (RSP11110)
  6. 0.353 Cherry (RSP11143)
  7. 0.350 Golden Goat 2 (RSP10991)
  8. 0.349 RKM-2018-028 (RSP11120)
  9. 0.348 RKM-2018-023 (RSP11115)
  10. 0.347 RKM-2018-022 (RSP11114)
  11. 0.346 JL yellow (RSP11075)
  12. 0.346 Cherry (RSP11142)
  13. 0.345 Skunk 18 (RSP11038)
  14. 0.343 Cbot-2019-004 (RSP11132)
  15. 0.336 Blueberry Cheesecake (RSP10672)
  16. 0.336 RKM-2018-032 (RSP11124)
  17. 0.334 RKM-2018-019 (RSP11111)
  18. 0.332 RKM-2018-003 (RSP11094)
  19. 0.327 Black Beauty (RSP11035)
  20. 0.327 RKM-2018-006 (RSP11097)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448780
Overlapping SNPs:
43
Concordance:
28

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495248
Overlapping SNPs:
3
Concordance:
3

Blockchain Registration Information

Transaction ID
383f0c866999546872edb65563d8298d5f52bb50763413ff9c9c359466a7688d
Stamping Certificate
Download PDF (873.5 KB)
SHASUM Hash
fe2b64ed3bd5761c8ac29eda8187a4e30a5d31ffaa31cc527eeacebf1947fb3b
QR code for RSP10976

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