Advanced Strain Search

Afghan_Kush_2

SRR 3294441

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
Unknown

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: 1.23%
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: 0.0195
male female SRR3294441

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)
PHL-2 c.1540A>G p.Thr514Ala missense variant moderate contig2621 340818

IGV: Start, Jump

A/G
NGS:
0.042
C90:
0.282
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.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-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.127T>G p.Ser43Ala missense variant moderate contig95 1989794

IGV: Start, Jump

T/G
NGS:
0.721
C90:
0.000
PIE1-2

UniProt

c.5932A>G p.Ile1978Val missense variant moderate contig1460 1185552

IGV: Start, Jump

T/C
NGS:
0.061
C90:
0.268
GGR

UniProt

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

IGV: Start, Jump

G/A
NGS:
0.018
C90:
0.000
GGR

UniProt

c.704A>T p.His235Leu missense variant moderate contig2282 549696

IGV: Start, Jump

A/T
NGS:
0.121
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.033 0.067 0.100 0.133
closely related moderately related distantly related
  1. 0.050 UC 167 (SRR14419585)
  2. 0.068 Blue Dream (RSP11017)
  3. 0.079 (SRR3294430)
  4. 0.083 UC 27 (SRR14419817)
  5. 0.083 B52 (SRR14708255)
  6. 0.083 Ruderalis Indica (SRR14708267)
  7. 0.086 UC 21 (SRR14419861)
  8. 0.088 Electra (RSP11366)
  9. 0.089 UC 445 (SRR14419766)
  10. 0.091 UC 32 (SRR14419761)
  11. 0.091 R1in136 (SRR14708237)
  12. 0.095 Blue Dream (RSP11007)
  13. 0.096 Rest (RSP11377)
  14. 0.097 UC 46 (SRR14419703)
  15. 0.097 UC 70 (SRR14419679)
  16. 0.100 UC 168 (SRR14419584)
  17. 0.100 Alpine Rocket (SRR14708266)
  18. 0.103 (SRR3294451)
  19. 0.106 Lemon OG Haze (RSP11977)
  20. 0.109 Triangle Kush x Square Wave BX (RSP12100)

Most genetically distant strains (All Samples)

0 0.108 0.217 0.325 0.433
closely related moderately related distantly related
  1. 0.413 80E (RSP11213)
  2. 0.407 JL 4th Gen 2 (RSP11194)
  3. 0.400 80E (RSP11211)
  4. 0.396 80E (RSP11212)
  5. 0.395 Feral (RSP10890)
  6. 0.376 Feral (RSP10891)
  7. 0.375 JL 3rd Gen Mother (RSP11214)
  8. 0.368 Carmaleonte (RSP11207)
  9. 0.367 JL 4th Gen 5 (RSP11199)
  10. 0.358 JL 3rd Gen Father (RSP11196)
  11. 0.355 Fedora 17 (RSP10661)
  12. 0.352 JL 4th Gen 1 (RSP11193)
  13. 0.351 Northern Lights (RSP11501)
  14. 0.349 Diana (RSP10235)
  15. 0.346 Carmagnola USO 31 (RSP11204)
  16. 0.344 Feral (RSP11205)
  17. 0.343 Fedora 17 (RSP11203)
  18. 0.343 Tiger Tail 30 (RSP11484)
  19. 0.342 Tiborszallasie (RSP11210)
  20. 0.342 Feral (RSP11206)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR8347222
Overlapping SNPs:
6
Concordance:
6

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495158
Overlapping SNPs:
3
Concordance:
3

Blockchain Registration Information

SHASUM Hash
f0a7eb8ec92b2bd9e7a9ecc71daa2b8e715c014b24327853bb3acc1135a824cf
QR code for SRR3294441

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