Advanced Strain Search

Square Wave

RSP 11344

Grower: Happy Valley

Summary

Square Wave (RSP11344/Happy Valley) is a genetic Type I plant and its genetics appear rare. The sample's closest relative in the database is Pure Power Plant (RSP11265/Kyle Russell) and it is a potential sibling. The heterozygosity rate is 1.16% which is average (63.3 percentile).

General Information

Accession Date
October 17, 2019
Reported Plant Sex
Female
DNA Extracted From
Stem

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: Rare
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: 1.16%
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: 0.0486
male female RSP11344

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)

Gene HGVS.c HGVS.p Annotation Annotation Impact Contig Contig Pos Ref/Alt Var Freq
THCAS c.998C>G p.Pro333Arg missense variant moderate contig741 4416830

IGV: Start, Jump

G/C
NGS:
0.182
C90:
0.000

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
PKSG-2b

UniProt

c.1152T>A p.Asn384Lys missense variant moderate contig700 1950486

IGV: Start, Jump

A/T
NGS:
0.715
C90:
0.895
PKSG-2b

UniProt

c.1132C>G p.Leu378Val missense variant moderate contig700 1950506

IGV: Start, Jump

G/C
NGS:
0.717
C90:
0.000
PKSG-2b

UniProt

c.1117A>G p.Ile373Val missense variant moderate contig700 1950521

IGV: Start, Jump

T/C
NGS:
0.807
C90:
0.981
PKSG-2b

UniProt

c.948T>G p.Asp316Glu missense variant moderate contig700 1950690

IGV: Start, Jump

A/C
NGS:
0.456
C90:
0.000
PKSG-2b

UniProt

c.945T>G p.Ser315Arg missense variant moderate contig700 1950693

IGV: Start, Jump

A/C
NGS:
0.454
C90:
0.000
PKSG-2b

UniProt

c.944G>A p.Ser315Asn missense variant moderate contig700 1950694

IGV: Start, Jump

C/T
NGS:
0.445
C90:
0.000
PKSG-2b

UniProt

c.934C>G p.His312Asp missense variant moderate contig700 1950704

IGV: Start, Jump

G/C
NGS:
0.410
C90:
0.000
PKSG-2b

UniProt

c.31A>T p.Thr11Ser missense variant moderate contig700 1951851

IGV: Start, Jump

T/A
NGS:
0.844
C90:
0.880
PKSG-2b

UniProt

c.-2_1dupATA start lost & conservative inframe insertion high contig700 1951880

IGV: Start, Jump

A/ATAT
NGS:
0.410
C90:
0.000
DXR-2

UniProt

c.1319T>C p.Ile440Thr missense variant moderate contig380 285250

IGV: Start, Jump

A/G
NGS:
0.480
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.216A>T p.Lys72Asn missense variant moderate contig121 2828872

IGV: Start, Jump

A/T
NGS:
0.075
C90:
0.000
aPT4

UniProt

c.775delT p.Tyr259fs frameshift variant high contig121 2831380

IGV: Start, Jump

AT/A
NGS:
0.224
C90:
0.000
aPT4

UniProt

c.1168T>C p.Tyr390His missense variant moderate contig121 2833503

IGV: Start, Jump

T/C
NGS:
0.546
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-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

Nearest genetic relatives (All Samples)

0 0.067 0.133 0.200 0.267
closely related moderately related distantly related
  1. 0.201 Strawberry Cough (RSP11356)
  2. 0.204 Eran Almog 05MAY2017 (RSP10937)
  3. 0.214 Green Crack (RSP12099)
  4. 0.216 Pure Power Plant (RSP11265)
  5. 0.217 Strawberry (RSP12095)
  6. 0.222 RKM-2018-008 (RSP11099)
  7. 0.226 LEMONCAKE (RSP11340)
  8. 0.227 Goin Bananas (RSP12509)
  9. 0.229 Skunk#18 (RSP11030)
  10. 0.233 GMO x Poison Momosa (RSP12626)
  11. 0.233 JABBA S STASH (RSP11348)
  12. 0.233 Dominion Skunk (RSP11354)
  13. 0.234 Miss X (RSP10999)
  14. 0.234 Golden Goat 2 (RSP10991)
  15. 0.235 Skunk#18 (RSP11038)
  16. 0.236 Durban Poison #1 (RSP11013)
  17. 0.236 Blueberry Cheesecake (RSP10684)
  18. 0.237 Serious Happiness (RSP10763)
  19. 0.238 CPH (RSP11367)
  20. 0.241 Afm (RSP12622)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
closely related moderately related distantly related
  1. 0.467 Chematonic -Cannatonic x Chemdawg- (RSP11394)
  2. 0.461 Tanao Sri -46- (RSP11486)
  3. 0.457 Cherry Blossom (RSP11306)
  4. 0.457 Cherry Blossom (RSP11323)
  5. 0.454 Cherry Blossom (RSP11328)
  6. 0.443 Cherry Blossom (RSP11298)
  7. 0.433 Cherry Blossom (RSP11318)
  8. 0.432 Cherry Blossom (RSP11322)
  9. 0.432 Cherry Blossom (RSP11309)
  10. 0.431 Cherry Blossom (RSP11325)
  11. 0.430 Cherry Blossom (RSP11301)
  12. 0.427 Cherry Blossom (RSP11330)
  13. 0.422 JL yellow (RSP11075)
  14. 0.419 Unknown--Cherry Wine---003- (RSP11270)
  15. 0.410 Wife (RSP11148)
  16. 0.409 AVIDEKEL USA (RSP11169)
  17. 0.404 JL 3rd Gen Mother (RSP11214)
  18. 0.403 Cherry Blossom (RSP11317)
  19. 0.402 Feral (RSP10890)
  20. 0.402 Cherry Blossom (RSP11312)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR8346391
Overlapping SNPs:
66
Concordance:
47

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495160
Overlapping SNPs:
3
Concordance:
3

Blockchain Registration Information

Transaction ID
d37e16a21012357c3cde02867bd5439a6deb50d1f4af1fb3fd5565ea04d10c0d
Stamping Certificate
Download PDF (847.0 KB)
SHASUM Hash
c96ffd7597434e00a3af1b0eede704fae5c54f2fdaffc32970af0297e329d7fc
QR code for RSP11344

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