Feral

RSP 10890

Grower: John McKay-Colorado State University

General Information

Sample Name
Merino_S_10_CSU
Accession Date
May 3, 2017
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: 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 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: 1.07%
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: 0.0455
male female RSP10890

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)

GPPs1

UniProt

c.160A>G p.Lys54Glu missense variant moderate contig676 168409

IGV: Start, Jump

A/G
NGS:
0.026
C90:
0.000
PKSG-4a

UniProt

c.37C>G p.Gln13Glu missense variant moderate contig700 1936734

IGV: Start, Jump

C/G
NGS:
0.031
C90:
0.000
PKSG-4a

UniProt

c.493G>A p.Gly165Ser missense variant moderate contig700 1937904

IGV: Start, Jump

G/A
NGS:
0.103
C90:
0.000
PKSG-4a

UniProt

c.1188_1190delCAA p.Asn397del disruptive inframe deletion moderate contig700 1938598

IGV: Start, Jump

CCAA/C
NGS:
0.002
C90:
0.000
PKSG-4a

UniProt

c.1192T>A p.Tyr398Asn missense variant moderate contig700 1938603

IGV: Start, Jump

T/A
NGS:
0.002
C90:
0.000
PKSG-2a

UniProt

c.1117A>G p.Ile373Val missense variant moderate contig700 1944273

IGV: Start, Jump

T/C
NGS:
0.101
C90:
0.967
PKSG-2a

UniProt

c.948T>G p.Asp316Glu missense variant moderate contig700 1944442

IGV: Start, Jump

A/C
NGS:
0.079
C90:
0.000
PKSG-2a

UniProt

c.945T>G p.Ser315Arg missense variant moderate contig700 1944445

IGV: Start, Jump

A/C
NGS:
0.079
C90:
0.000
PKSG-2a

UniProt

c.944G>A p.Ser315Asn missense variant moderate contig700 1944446

IGV: Start, Jump

C/T
NGS:
0.079
C90:
0.000
PKSG-2a

UniProt

c.934C>G p.His312Asp missense variant moderate contig700 1944456

IGV: Start, Jump

G/C
NGS:
0.070
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.67A>T p.Ile23Phe missense variant moderate contig700 1951815

IGV: Start, Jump

T/A
NGS:
0.033
C90:
0.325
PKSG-4b

UniProt

c.544G>T p.Gly182Trp missense variant moderate contig700 2721129

IGV: Start, Jump

C/A
NGS:
0.055
C90:
0.000
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.353_354insCC p.Gly119fs frameshift variant high contig700 2721319

IGV: Start, Jump

T/TGG
NGS:
0.175
C90:
0.000
PKSG-4b

UniProt

c.338G>A p.Gly113Glu missense variant moderate contig700 2721335

IGV: Start, Jump

C/T
NGS:
0.046
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.80A>G p.Lys27Arg missense variant moderate contig121 2828736

IGV: Start, Jump

A/G
NGS:
0.061
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.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.1168T>C p.Tyr390His missense variant moderate contig121 2833503

IGV: Start, Jump

T/C
NGS:
0.546
C90:
0.000
aPT1

UniProt

c.95_97delGTT p.Cys32del disruptive inframe deletion moderate contig121 2835800

IGV: Start, Jump

ATGT/A
NGS:
0.118
C90:
0.311
aPT1

UniProt

c.160A>C p.Thr54Pro missense variant moderate contig121 2835867

IGV: Start, Jump

A/C
NGS:
0.086
C90:
0.048
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.670T>A p.Ser224Thr missense variant moderate contig121 2840278

IGV: Start, Jump

T/A
NGS:
0.077
C90:
0.000
aPT1

UniProt

c.727G>T p.Glu243* stop gained high contig121 2841362

IGV: Start, Jump

G/T
NGS:
0.127
C90:
0.100
aPT1

UniProt

c.864C>G p.Asn288Lys missense variant moderate contig121 2842407

IGV: Start, Jump

C/G
NGS:
0.075
C90:
0.062
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 0.067 0.133 0.200 0.267
clone distance sibling distance more distant
  1. 0.164 Feral (RSP10891)
  2. 0.169 Feral (RSP10892)
  3. 0.175 Feral (RSP11205)
  4. 0.219 Carmagnola (RSP10978)
  5. 0.221 Carmagnola (RSP10976)
  6. 0.222 Tisza (RSP11044)
  7. 0.223 Carmagnola (RSP11039)
  8. 0.225 Carmagnola (RSP11037)
  9. 0.226 Carmagnola (RSP10982)
  10. 0.227 Carmagnola (RSP10977)
  11. 0.228 Tisza (RSP11045)
  12. 0.231 Feral (RSP11206)
  13. 0.233 KYRG-21 (RSP11053)
  14. 0.234 Carmagnola (RSP10980)
  15. 0.237 Tisza (RSP10659)
  16. 0.237 Ivory (RSP10668)
  17. 0.238 Carmagnola (RSP10979)
  18. 0.240 Lovrin (RSP10658)
  19. 0.241 Diana (RSP10235)
  20. 0.242 Carmagnola (RSP10655)

Nearest genetic relatives (Base Tree)

0 0.083 0.167 0.250 0.333
clone distance sibling distance more distant
  1. 0.219 Tisza (RSP11044)
  2. 0.235 Carmagnola (RSP11037)
  3. 0.237 Tisza (RSP10659)
  4. 0.242 Lovrin (RSP10658)
  5. 0.243 Carmagnola (RSP10979)
  6. 0.243 Fedora 17 (RSP10661)
  7. 0.249 Ivory (RSP10668)
  8. 0.250 Futura 75 (RSP10664)
  9. 0.254 USO 31 (RSP10981)
  10. 0.255 Kyrgyz Gold (RSP11054)
  11. 0.256 Monoica (RSP10241)
  12. 0.260 Jiangji (RSP10653)
  13. 0.262 Santhica27 (RSP11047)
  14. 0.263 KYRG-11 (RSP11051)
  15. 0.264 Tygra (RSP10667)
  16. 0.300 Kimbo Slice (RSP10997)
  17. 0.306 RKM-2018-029 (RSP11121)
  18. 0.316 Recon (RSP10755)
  19. 0.324 CST (RSP11002)
  20. 0.327 Hermaphrodite ResearchSample2 (RSP11050)

Most genetically distant strains (All Samples)

0 0.125 0.250 0.375 0.500
clone distance sibling distance more distant
  1. 0.469 Cherry Blossom (RSP11318)
  2. 0.460 Cherry Blossom (RSP11300)
  3. 0.451 Cherry Blossom (RSP11323)
  4. 0.445 Cherry Blossom (RSP11312)
  5. 0.445 Cherry Blossom (RSP11331)
  6. 0.440 Cherry Blossom (RSP11311)
  7. 0.437 Cherry Blossom (RSP11301)
  8. 0.437 Cherry Blossom (RSP11325)
  9. 0.437 Cherry Blossom (RSP11328)
  10. 0.435 Cherry Blossom (RSP11299)
  11. 0.434 Cherry Blossom (RSP11324)
  12. 0.434 Cherry Blossom (RSP11332)
  13. 0.433 Cherry Blossom (RSP11308)
  14. 0.433 Cherry Blossom (RSP11334)
  15. 0.432 Wife (RSP11148)
  16. 0.431 Cherry Blossom (RSP11335)
  17. 0.431 Cherry Blossom (RSP11302)
  18. 0.428 Escape Velocity (RSP11165)
  19. 0.428 Cherry Blossom (RSP11333)
  20. 0.425 Cherry Blossom (RSP11298)

Most genetically distant strains (Base Tree)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.404 Cbot-2019-005 (RSP11133)
  2. 0.394 RKM-2018-028 (RSP11120)
  3. 0.388 RKM-2018-006 (RSP11097)
  4. 0.386 UP Sunrise (RSP10989)
  5. 0.385 Kush Hemp E1 (RSP11128)
  6. 0.379 Skunk 18 (RSP11038)
  7. 0.376 RKM-2018-018 (RSP11110)
  8. 0.376 RKM-2018-022 (RSP11114)
  9. 0.374 RKM-2018-027 (RSP11119)
  10. 0.372 RKM-2018-032 (RSP11124)
  11. 0.371 Cbot-2019-001 (RSP11129)
  12. 0.370 RKM-2018-002 (RSP11093)
  13. 0.367 RKM-2018-003 (RSP11094)
  14. 0.367 Cherry (RSP11142)
  15. 0.367 Blueberry Cheesecake (RSP10672)
  16. 0.363 Sour Raspberry (RSP10551)
  17. 0.363 JL yellow (RSP11075)
  18. 0.363 Cbot-2019-004 (RSP11132)
  19. 0.362 Hermaphrodite Research Sample1 (RSP11049)
  20. 0.361 RKM-2018-023 (RSP11115)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4450098
Overlapping SNPs:
105
Concordance:
65

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495248
Overlapping SNPs:
3
Concordance:
3

Blockchain Registration Information

Transaction ID
4dd249199888858d444a2d66126244dbe82126ce81251b34351365124bb10313
Stamping Certificate
Download PDF (854.5 KB)
SHASUM Hash
105f22ccf92e1fd13af9b3aec07c1fc94115b99333826ccb3b0d5f684392a58d
QR code for RSP10890

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