Advanced Strain Search

Afghan_Kush_3

SRR 3294451

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 II

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: 1.36%
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: 0.0590
male female SRR3294451

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)
GPPs1

UniProt

c.916delG p.Val306fs frameshift variant high contig676 169802

IGV: Start, Jump

TG/T
NGS:
0.000
C90:
0.000
PHL-2 c.2756A>C p.Glu919Ala missense variant moderate contig2621 342799

IGV: Start, Jump

A/C
NGS:
0.064
C90:
0.675
ELF3

UniProt

c.1230-2_1230-1delAG splice acceptor variant & intron variant high contig97 243676

IGV: Start, Jump

TAG/T
NGS:
0.088
C90:
0.450
ELF3

UniProt

c.2141C>G p.Pro714Arg missense variant moderate contig97 244972

IGV: Start, Jump

C/G
NGS:
0.088
C90:
0.335
aPT4

UniProt

c.16G>A p.Val6Ile missense variant moderate contig121 2828672

IGV: Start, Jump

G/A
NGS:
0.158
C90:
0.000
aPT4

UniProt

c.97T>C p.Tyr33His missense variant moderate contig121 2828753

IGV: Start, Jump

T/C
NGS:
0.439
C90:
0.000
aPT4

UniProt

c.153A>C p.Lys51Asn missense variant moderate contig121 2828809

IGV: Start, Jump

A/C
NGS:
0.375
C90:
0.000
aPT4

UniProt

c.202T>A p.Leu68Ile missense variant moderate contig121 2828858

IGV: Start, Jump

T/A
NGS:
0.068
C90:
0.000
aPT4

UniProt

c.235_236delGT p.Val79fs frameshift variant high contig121 2829030

IGV: Start, Jump

ATG/A
NGS:
0.417
C90:
0.000
aPT4

UniProt

c.238delT p.Ser80fs frameshift variant high contig121 2829034

IGV: Start, Jump

AT/A
NGS:
0.421
C90:
0.000
aPT4

UniProt

c.302A>G p.Asn101Ser missense variant moderate contig121 2829099

IGV: Start, Jump

A/G
NGS:
0.349
C90:
0.000
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.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.136G>A p.Val46Ile missense variant moderate contig1891 889256

IGV: Start, Jump

C/T
NGS:
0.088
C90:
0.593
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

Nearest genetic relatives (All Samples)

0 0.033 0.067 0.100 0.133
closely related moderately related distantly related
  1. 0.033 Triangle Kush x Square Wave BX (RSP12100)
  2. 0.044 UC 70 (SRR14419679)
  3. 0.050 UC 62 (SRR14419687)
  4. 0.052 UC 167 (SRR14419585)
  5. 0.052 UC 46 (SRR14419703)
  6. 0.054 UC 74 (SRR14419674)
  7. 0.056 UC 141 (SRR14419609)
  8. 0.056 UC 493 (SRR14419740)
  9. 0.057 (SRR3294430)
  10. 0.071 UC 170 (SRR14419582)
  11. 0.076 UC 32 (SRR14419761)
  12. 0.078 UC 500 (SRR14419736)
  13. 0.078 UC 34 (SRR14419739)
  14. 0.081 UC 27 (SRR14419817)
  15. 0.083 VIR 483 (SRR14708238)
  16. 0.086 UC 89 (SRR14419661)
  17. 0.086 UC 86 (SRR14419663)
  18. 0.086 UC 445 (SRR14419766)
  19. 0.088 UC 18 (SRR14419894)
  20. 0.091 UC 155 (SRR14419597)

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. 0.387 Fedora 17 (RSP10661)
  3. 0.384 Tanao Sri 46 (RSP11486)
  4. 0.382 Monoica (RSP10241)
  5. 0.379 JL 4th Gen 1 (RSP11193)
  6. 0.377 JL 3rd Gen Father (RSP11196)
  7. 0.368 Cherry Blossom (RSP11306)
  8. 0.366 Feral (RSP11205)
  9. 0.365 Cherry Blossom (RSP11317)
  10. 0.362 80E (RSP11211)
  11. 0.358 Carmaleonte (RSP11207)
  12. 0.357 Carmagnola (RSP11037)
  13. 0.352 Tiger Tail 30 (RSP11484)
  14. 0.352 USO 31 (RSP10983)
  15. 0.349 Carmagnola (RSP10977)
  16. 0.348 JL yellow (RSP11075)
  17. 0.345 JL 3rd Gen Mother (RSP11214)
  18. 0.344 Santhica27 (RSP11047)
  19. 0.343 80E (RSP11212)
  20. 0.343 JL 4th Gen 6 (RSP11200)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448396
Overlapping SNPs:
3
Concordance:
3

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495158
Overlapping SNPs:
3
Concordance:
3

Blockchain Registration Information

SHASUM Hash
a27d2fb1cfa0aa38c49ab17c93ff760e180c361f111f27310b8a146ce513a8f0
QR code for SRR3294451

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