Badger

RSP 11614

Grower: WI Greenhouse/WI crop Innovation Center

General Information

Sample Name
Badger 062220
Accession Date
July 6, 2020
Reported Plant Sex
Female

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: Uncommon
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 III

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: 1.31%
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: 0.0560
male female RSP11614

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
CBDAS c.1420A>C p.Lys474Gln missense variant moderate contig1772 2083646

IGV: Start, Jump

A/C
NGS:
0.132
C90:
0.813

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.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
PKSG-4b

UniProt

c.556A>G p.Arg186Gly missense variant & splice region variant moderate contig700 2721117

IGV: Start, Jump

T/C
NGS:
0.022
C90:
0.000
PKSG-4b

UniProt

c.496A>G p.Lys166Glu missense variant moderate contig700 2721177

IGV: Start, Jump

T/C
NGS:
0.651
C90:
0.684
PKSG-4b

UniProt

c.489delT p.Phe163fs frameshift variant high contig700 2721183

IGV: Start, Jump

CA/C
NGS:
0.792
C90:
0.761
PKSG-4b

UniProt

c.485A>G p.Lys162Arg missense variant moderate contig700 2721188

IGV: Start, Jump

T/C
NGS:
0.643
C90:
0.301
PKSG-4b

UniProt

c.431T>G p.Val144Gly missense variant moderate contig700 2721242

IGV: Start, Jump

A/C
NGS:
0.575
C90:
0.679
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

Nearest genetic relatives (All Samples)

0 0.050 0.100 0.150 0.200
clone distance sibling distance more distant
  1. 0.085 Electra (RSP11366)
  2. 0.119 Doug s Varin (RSP11243)
  3. 0.123 Lift (RSP11378)
  4. 0.127 Suver Haze (RSP11364)
  5. 0.128 Serious Happiness (RSP10763)
  6. 0.133 Joy (RSP11380)
  7. 0.148 Domnesia (RSP11184)
  8. 0.156 FL30 (RSP11361)
  9. 0.159 JL X NSPM1 14 (RSP11473)
  10. 0.160 Blue Dream (RSP11017)
  11. 0.161 RINGO S ANGEL (RSP10085)
  12. 0.165 Blue Dream (RSP11004)
  13. 0.166 Blue Dream (RSP11010)
  14. 0.170 Blueberry Cheesecake (RSP10684)
  15. 0.173 Blue Dream (RSP11007)
  16. 0.173 Trump x Trump (RSP11466)
  17. 0.174 Cherry Blossom (RSP11320)
  18. 0.176 Rest (RSP11377)
  19. 0.178 Super Blue Dream (RSP11011)
  20. 0.180 Lifter (RSP11365)

Nearest genetic relatives (Base Tree)

0 0.075 0.150 0.225 0.300
clone distance sibling distance more distant
  1. 0.174 Blueberry Cheesecake (RSP10684)
  2. 0.196 Liberty Haze (RSP11000)
  3. 0.208 UP Sunrise (RSP10989)
  4. 0.222 Durban Poison (RSP11014)
  5. 0.237 QUEEN JESUS (RSP10105)
  6. 0.245 Golden Goat 2 (RSP10991)
  7. 0.245 Recon (RSP10755)
  8. 0.254 Blueberry Cheesecake (RSP10672)
  9. 0.255 Blue Dream (RSP11033)
  10. 0.258 Cherry (RSP11143)
  11. 0.263 Cbot-2019-001 (RSP11129)
  12. 0.268 Gold Cracker (RSP11048)
  13. 0.268 Kimbo Slice (RSP10997)
  14. 0.272 RKM-2018-020 (RSP11112)
  15. 0.273 CST (RSP11002)
  16. 0.274 RKM-2018-031 (RSP11123)
  17. 0.275 RKM-2018-027 (RSP11119)
  18. 0.282 Hermaphrodite Research Sample1 (RSP11049)
  19. 0.282 RKM-2018-005 (RSP11096)
  20. 0.282 Blueberry Cheesecake (RSP10680)

Most genetically distant strains (All Samples)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.412 80E (RSP11213)
  2. 0.399 JL yellow (RSP11075)
  3. 0.395 80E (RSP11211)
  4. 0.384 80E (RSP11212)
  5. 0.379 Kush Hemp E1 (RSP11128)
  6. 0.372 Chem 91 (RSP11185)
  7. 0.368 JL 3rd Gen Mother (RSP11214)
  8. 0.365 JL 3rd Gen Father (RSP11196)
  9. 0.365 Feral (RSP11205)
  10. 0.362 Tanao Sri 46 (RSP11486)
  11. 0.362 White Label 1 (RSP11336)
  12. 0.361 JL 4th Gen 6 (RSP11200)
  13. 0.357 USO31 (RSP10233)
  14. 0.351 Abacus (RSP11266)
  15. 0.351 JL 3rd Gen Mother (RSP11197)
  16. 0.350 RKM-2018-012 (RSP11103)
  17. 0.350 Chematonic Cannatonic x Chemdawg (RSP11394)
  18. 0.349 Star Dawg (RSP11352)
  19. 0.349 JL 4th Gen 5 (RSP11199)
  20. 0.348 Northern Lights (RSP11501)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.386 JL yellow (RSP11075)
  2. 0.384 Kush Hemp E1 (RSP11128)
  3. 0.359 Carmagnola (RSP10979)
  4. 0.358 RKM-2018-026 (RSP11118)
  5. 0.356 RKM-2018-002 (RSP11093)
  6. 0.353 Carmagnola (RSP11037)
  7. 0.349 Feral (RSP10890)
  8. 0.349 Monoica (RSP10241)
  9. 0.343 Futura 75 (RSP10664)
  10. 0.342 Cbot-2019-005 (RSP11133)
  11. 0.341 Ivory (RSP10668)
  12. 0.340 Kyrgyz Gold (RSP11054)
  13. 0.340 RKM-2018-022 (RSP11114)
  14. 0.338 Lovrin (RSP10658)
  15. 0.337 Fedora 17 (RSP10661)
  16. 0.337 Skunk 18 (RSP11038)
  17. 0.336 Santhica27 (RSP11047)
  18. 0.334 KYRG-11 (RSP11051)
  19. 0.334 Skywalker OG (RSP10837)
  20. 0.325 USO 31 (RSP10981)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448699
Overlapping SNPs:
59
Concordance:
39

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495173
Overlapping SNPs:
6
Concordance:
6

Blockchain Registration Information

Transaction ID
deb2f3d9f39f0e67b4012ce64c96ce5e96d7702f0d2f85f3948048f4158b70d1
Stamping Certificate
Download PDF (39.4 KB)
SHASUM Hash
e2869076ead761ca7596b6946389a531e6a20bf764ac41db7c38087133c8bfbc
QR code for RSP11614

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