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

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%

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

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:
0.001
C90:
0.000
PHL-2 c.2756A>C p.Glu919Ala missense variant moderate contig2621 342799

IGV: Start, Jump

A/C
NGS:
0.409
C90:
0.675
ELF3

UniProt

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

IGV: Start, Jump

TAG/T
NGS:
0.517
C90:
0.450
ELF3

UniProt

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

IGV: Start, Jump

C/G
NGS:
0.507
C90:
0.335
aPT4

UniProt

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

IGV: Start, Jump

G/A
NGS:
0.113
C90:
0.000
aPT4

UniProt

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

IGV: Start, Jump

T/C
NGS:
0.300
C90:
0.000
aPT4

UniProt

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

IGV: Start, Jump

A/C
NGS:
0.280
C90:
0.000
aPT4

UniProt

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

IGV: Start, Jump

T/A
NGS:
0.056
C90:
0.000
aPT4

UniProt

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

IGV: Start, Jump

ATG/A
NGS:
0.189
C90:
0.000
aPT4

UniProt

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

IGV: Start, Jump

AT/A
NGS:
0.190
C90:
0.000
aPT4

UniProt

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

IGV: Start, Jump

A/G
NGS:
0.153
C90:
0.000
aPT1

UniProt

c.406A>G p.Ile136Val missense variant moderate contig121 2839605

IGV: Start, Jump

A/G
NGS:
0.582
C90:
0.761
aPT1

UniProt

c.629C>T p.Thr210Ile missense variant moderate contig121 2840237

IGV: Start, Jump

C/T
NGS:
0.525
C90:
0.598
HDS-1

UniProt

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

IGV: Start, Jump

T/C
NGS:
0.584
C90:
0.861
HDS-1

UniProt

c.136G>A p.Val46Ile missense variant moderate contig1891 889256

IGV: Start, Jump

C/T
NGS:
0.372
C90:
0.593
HDS-1

UniProt

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

IGV: Start, Jump

G/C
NGS:
0.648
C90:
0.943
HDS-1

UniProt

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

IGV: Start, Jump

C/T
NGS:
0.481
C90:
0.646

Nearest genetic relatives (All Samples)

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 Afghan_Kush_1 (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)

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)

Blockchain Registration Information

SHASUM Hash
a27d2fb1cfa0aa38c49ab17c93ff760e180c361f111f27310b8a146ce513a8f0
QR code for SRR3294451

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