Advanced Strain Search

Afghan_Kush_1

SRR 3294430

Grower: University of Colorado Boulder, John Mendieta

General Information

Accession Date
February 7, 2016
Reported Plant Sex
Male

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: Common
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 I

File Downloads

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: 1.49%
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: 0.0621
male female SRR3294430

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.774G>A p.Met258Ile missense variant moderate contig700 1950864

IGV: Start, Jump

C/T
NGS:
0.366
C90:
0.947
FAD2-2

UniProt

c.172G>T p.Asp58Tyr missense variant moderate contig83 1803197

IGV: Start, Jump

C/A
NGS:
0.070
C90:
0.000
FAD2-2

UniProt

c.164A>G p.His55Arg missense variant moderate contig83 1803205

IGV: Start, Jump

T/C
NGS:
0.037
C90:
0.000
FAD2-2

UniProt

c.161T>A p.Leu54His missense variant moderate contig83 1803208

IGV: Start, Jump

A/T
NGS:
0.156
C90:
0.000
FAD2-2

UniProt

c.64G>T p.Ala22Ser missense variant moderate contig83 1803305

IGV: Start, Jump

C/A
NGS:
0.048
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
HDS-1

UniProt

c.1618A>G p.Ile540Val missense variant moderate contig1891 885936

IGV: Start, Jump

T/C
NGS:
0.099
C90:
0.861
HDS-1

UniProt

c.56C>G p.Ala19Gly missense variant moderate contig1891 889336

IGV: Start, Jump

G/C
NGS:
0.125
C90:
0.943
HDS-1

UniProt

c.35G>A p.Cys12Tyr missense variant moderate contig1891 889357

IGV: Start, Jump

C/T
NGS:
0.094
C90:
0.646
AAE1-3

UniProt

c.634G>C p.Gly212Arg missense variant moderate contig976 1083220

IGV: Start, Jump

C/G
NGS:
0.116
C90:
0.000
GGR

UniProt

c.679G>A p.Glu227Lys missense variant moderate contig2282 549671

IGV: Start, Jump

G/A
NGS:
0.018
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.033 0.067 0.100 0.133
closely related moderately related distantly related
  1. 0.019 UC 46 (SRR14419703)
  2. 0.033 UC 167 (SRR14419585)
  3. 0.047 Triangle Kush x Square Wave BX (RSP12100)
  4. 0.048 UC 32 (SRR14419761)
  5. 0.050 UC 34 (SRR14419739)
  6. 0.056 UC 49 (SRR14419701)
  7. 0.057 (SRR3294451)
  8. 0.059 UC 70 (SRR14419679)
  9. 0.062 Electra (RSP11366)
  10. 0.063 UC 71 (SRR14419677)
  11. 0.063 UC 21 (SRR14419861)
  12. 0.063 Lift (RSP11378)
  13. 0.065 UC 141 (SRR14419609)
  14. 0.071 Doug s Varin (RSP11243)
  15. 0.071 Blue Dream (RSP11010)
  16. 0.074 East side OG (RSP12089)
  17. 0.076 UC 18 (SRR14419894)
  18. 0.078 UC 62 (SRR14419687)
  19. 0.078 UC 48 (SRR14419702)
  20. 0.079 (SRR3294441)

Most genetically distant strains (All Samples)

0 0.100 0.200 0.300 0.400
closely related moderately related distantly related
  1. 0.380 80E (RSP11213)
  2. 0.362 JL 4th Gen 6 (RSP11200)
  3. 0.354 80E (RSP11212)
  4. 0.352 80E (RSP11211)
  5. 0.348 JL yellow (RSP11075)
  6. 0.345 JL 3rd Gen Mother (RSP11214)
  7. 0.339 Fedora 17 (RSP10661)
  8. 0.333 Carmaleonte (RSP11207)
  9. 0.329 IBE (SRR14708228)
  10. 0.328 JL 4th Gen 1 (RSP11193)
  11. 0.325 JL 4th Gen 5 (RSP11199)
  12. 0.324 Feral (RSP11205)
  13. 0.323 JL 3rd Gen Father (RSP11196)
  14. 0.315 Santhica27 (RSP11047)
  15. 0.312 Fedora 17 (RSP11203)
  16. 0.308 Santhica27 (RSP11046)
  17. 0.308 Monoica (RSP10241)
  18. 0.305 Northern Lights (RSP11501)
  19. 0.303 Santhica27 (RSP10056)
  20. 0.301 Tisza (RSP11044)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448184
Overlapping SNPs:
5
Concordance:
5

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495158
Overlapping SNPs:
1
Concordance:
1

Blockchain Registration Information

SHASUM Hash
619d08308a57f9afdccb0ffaf5ecd1b36487c4d88065f80362d61df38a477062
QR code for SRR3294430

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