VIR 37 - Novgorod-Seversky - cv

SRR 14708234

Grower: Lanzhou University, Guangpeng Ren

General Information

Sample Name
UNS
Accession Date
May 31, 2021
Reported Plant Sex
not reported

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 II

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: 1.52%
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: 0.0577
male female SRR14708234

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.896A>G p.Asn299Ser missense variant moderate contig676 169772

IGV: Start, Jump

A/G
NGS:
0.046
C90:
0.000
PHL-2 c.1540A>G p.Thr514Ala missense variant moderate contig2621 340818

IGV: Start, Jump

A/G
NGS:
0.042
C90:
0.282
PHL-2 c.2756A>C p.Glu919Ala missense variant moderate contig2621 342799

IGV: Start, Jump

A/C
NGS:
0.064
C90:
0.675
PHL-2 c.2783G>A p.Ser928Asn missense variant moderate contig2621 342826

IGV: Start, Jump

G/A
NGS:
0.107
C90:
0.890
PHL-2 c.3002A>G p.Tyr1001Cys missense variant moderate contig2621 343045

IGV: Start, Jump

A/G
NGS:
0.055
C90:
0.316
PHL-2 c.3027G>T p.Lys1009Asn missense variant moderate contig2621 343070

IGV: Start, Jump

G/T
NGS:
0.055
C90:
0.311
PHL-2 c.3033T>G p.Cys1011Trp missense variant moderate contig2621 343076

IGV: Start, Jump

T/G
NGS:
0.055
C90:
0.292
PHL-2 c.3209A>G p.Gln1070Arg missense variant moderate contig2621 343252

IGV: Start, Jump

A/G
NGS:
0.103
C90:
0.885
PHL-2 c.3379C>G p.His1127Asp missense variant moderate contig2621 343422

IGV: Start, Jump

C/G
NGS:
0.004
C90:
0.000
PHL-2 c.3380A>G p.His1127Arg missense variant moderate contig2621 343423

IGV: Start, Jump

A/G
NGS:
0.004
C90:
0.000
PHL-2 c.3381T>A p.His1127Gln missense variant moderate contig2621 343424

IGV: Start, Jump

T/A
NGS:
0.004
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.316+2T>A splice donor variant & intron variant high contig700 2723818

IGV: Start, Jump

A/T
NGS:
0.070
C90:
0.689
DXR-2

UniProt

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

IGV: Start, Jump

A/G
NGS:
0.480
C90:
0.000
ELF3

UniProt

c.574A>G p.Asn192Asp missense variant moderate contig97 242280

IGV: Start, Jump

A/G
NGS:
0.042
C90:
0.579
ELF3

UniProt

c.1466G>A p.Ser489Asn missense variant moderate contig97 244297

IGV: Start, Jump

G/A
NGS:
0.123
C90:
0.000
ELF3

UniProt

c.1630A>G p.Thr544Ala missense variant moderate contig97 244461

IGV: Start, Jump

A/G
NGS:
0.103
C90:
0.545
aPT1

UniProt

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

IGV: Start, Jump

C/T
NGS:
0.561
C90:
0.598
AAE1-2

UniProt

c.205T>A p.Ser69Thr missense variant moderate contig81 209167

IGV: Start, Jump

T/A
NGS:
0.013
C90:
0.000
AAE1-2

UniProt

c.1415G>A p.Ser472Asn missense variant moderate contig81 210377

IGV: Start, Jump

G/A
NGS:
0.070
C90:
0.000
AAE1-2

UniProt

c.1417A>G p.Thr473Ala missense variant moderate contig81 210379

IGV: Start, Jump

A/G
NGS:
0.070
C90:
0.000
AAE1-2

UniProt

c.1434G>T p.Glu478Asp missense variant moderate contig81 210396

IGV: Start, Jump

G/T
NGS:
0.075
C90:
0.000
AAE1-2

UniProt

c.1541T>C p.Val514Ala missense variant moderate contig81 210503

IGV: Start, Jump

T/C
NGS:
0.050
C90:
0.000
PHL-1

UniProt

c.2623A>G p.Thr875Ala missense variant moderate contig1439 1487174

IGV: Start, Jump

T/C
NGS:
0.123
C90:
0.000
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
PIE1-2

UniProt

c.5932A>G p.Ile1978Val missense variant moderate contig1460 1185552

IGV: Start, Jump

T/C
NGS:
0.061
C90:
0.268
PIE1-2

UniProt

c.2027A>T p.Gln676Leu missense variant moderate contig1460 1190013

IGV: Start, Jump

T/A
NGS:
0.004
C90:
0.014
FT

UniProt

c.175C>G p.Leu59Val missense variant moderate contig1561 3124599

IGV: Start, Jump

C/G
NGS:
0.004
C90:
0.000
FT

UniProt

c.276_277insGGTTTCCCTAA p.Met93fs frameshift variant & splice region variant high contig1561 3125016

IGV: Start, Jump

T/TAGGTTTCCCTA
NGS:
0.000
C90:
0.000
FT

UniProt

c.278+1G>T splice donor variant & intron variant high contig1561 3125020

IGV: Start, Jump

G/T
NGS:
0.002
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.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.757G>T p.Val253Leu missense variant moderate contig121 2831364

IGV: Start, Jump

G/T
NGS:
0.039
C90:
0.000
FLD

UniProt

c.2831A>G p.Glu944Gly missense variant moderate contig1450 2044201

IGV: Start, Jump

T/C
NGS:
0.011
C90:
0.000
AAE1-3

UniProt

c.655C>T p.Pro219Ser missense variant moderate contig976 1083199

IGV: Start, Jump

G/A
NGS:
0.007
C90:
0.000
AAE1-3

UniProt

c.635G>A p.Gly212Asp missense variant moderate contig976 1083219

IGV: Start, Jump

C/T
NGS:
0.007
C90:
0.000
AAE1-3

UniProt

c.634G>C p.Gly212Arg missense variant moderate contig976 1083220

IGV: Start, Jump

C/G
NGS:
0.116
C90:
0.000
AAE1-3

UniProt

c.12G>A p.Met4Ile missense variant moderate contig976 1084063

IGV: Start, Jump

C/T
NGS:
0.007
C90:
0.000
AAE1-3

UniProt

c.11T>C p.Met4Thr missense variant moderate contig976 1084064

IGV: Start, Jump

A/G
NGS:
0.007
C90:
0.000
GGR

UniProt

c.456T>A p.His152Gln missense variant moderate contig2282 549448

IGV: Start, Jump

T/A
NGS:
0.068
C90:
0.000
GGR

UniProt

c.460G>A p.Asp154Asn missense variant moderate contig2282 549452

IGV: Start, Jump

G/A
NGS:
0.070
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.050 0.100 0.150 0.200
clone distance sibling distance more distant
  1. 0.153 Lift (RSP11378)
  2. 0.154 Electra (RSP11366)
  3. 0.163 Badger (RSP11614)
  4. 0.164 Serious Happiness (RSP10763)
  5. 0.167 Durban Poison 1 (RSP10996)
  6. 0.167 Durban Poison 1 (RSP11013)
  7. 0.172 Doug s Varin (RSP11243)
  8. 0.177 Miss X (RSP10999)
  9. 0.182 VIR 469 (SRR14708242)
  10. 0.183 Super Blue Dream (RSP11011)
  11. 0.183 AOAC MI 508 (RSP11750)
  12. 0.183 Tygra (RSP10667)
  13. 0.184 Rest (RSP11377)
  14. 0.185 VIR 483 (SRR14708239)
  15. 0.188 Kompolti (SRR14708277)
  16. 0.189 Blueberry Cheesecake (RSP10684)
  17. 0.189 AOAC MI 545 (RSP11756)
  18. 0.190 Blue Dream (RSP11010)
  19. 0.191 Blue Dream (RSP11006)
  20. 0.192 VIR 469 (SRR14708243)

Nearest genetic relatives (Base Tree)

0 0.075 0.150 0.225 0.300
clone distance sibling distance more distant
  1. 0.200 Tisza (RSP11044)
  2. 0.221 Blueberry Cheesecake (RSP10684)
  3. 0.222 Liberty Haze (RSP11000)
  4. 0.236 Recon (RSP10755)
  5. 0.237 Tygra (RSP10667)
  6. 0.245 Santhica27 (RSP11047)
  7. 0.250 Tisza (RSP10659)
  8. 0.250 Hermaphrodite ResearchSample2 (RSP11050)
  9. 0.252 Carmagnola (RSP11037)
  10. 0.253 Cbot-2019-006 (RSP11134)
  11. 0.253 Lovrin (RSP10658)
  12. 0.261 Durban Poison (RSP11014)
  13. 0.262 Golden Goat 2 (RSP10991)
  14. 0.263 Kimbo Slice (RSP10997)
  15. 0.271 QUEEN JESUS (RSP10105)
  16. 0.274 RKM-2018-019 (RSP11111)
  17. 0.274 RKM-2018-009 (RSP11100)
  18. 0.275 UP Sunrise (RSP10989)
  19. 0.275 RKM-2018-005 (RSP11096)
  20. 0.276 RKM-2018-031 (RSP11123)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.445 JL 4th Gen 5 (RSP11199)
  2. 0.436 JL yellow (RSP11075)
  3. 0.419 JL 3rd Gen Mother (RSP11214)
  4. 0.397 Chematonic Cannatonic x Chemdawg (RSP11394)
  5. 0.396 Northern Lights (RSP11501)
  6. 0.394 JL 2 (RSP11076)
  7. 0.386 JL 4th Gen 6 (RSP11200)
  8. 0.381 JL 3rd Gen Mother (RSP11197)
  9. 0.381 JL 4th Gen 1 (RSP11193)
  10. 0.375 JL 4th Gen 4 (RSP11198)
  11. 0.374 Star Dawg (RSP11352)
  12. 0.367 Tanao Sri-white 80 (RSP11621)
  13. 0.364 JL 3rd Gen Father (RSP11196)
  14. 0.362 Red Eye OG (RSP11190)
  15. 0.362 Right Mark (RSP11628)
  16. 0.359 UP Sunset (RSP11256)
  17. 0.354 Tanao Sri-white 79 (RSP11620)
  18. 0.353 Gorilla Glue (RSP11493)
  19. 0.353 Tanao Sri 46 (RSP11486)
  20. 0.353 Skunk 18 (RSP11038)

Most genetically distant strains (Base Tree)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.455 JL yellow (RSP11075)
  2. 0.375 RKM-2018-002 (RSP11093)
  3. 0.366 Cbot-2019-004 (RSP11132)
  4. 0.359 RKM-2018-003 (RSP11094)
  5. 0.349 Skywalker OG (RSP10837)
  6. 0.347 RKM-2018-026 (RSP11118)
  7. 0.347 Monoica (RSP10241)
  8. 0.345 RKM-2018-034 (RSP11126)
  9. 0.343 Skunk 18 (RSP11038)
  10. 0.341 RKM-2018-029 (RSP11121)
  11. 0.338 Black Beauty (RSP11035)
  12. 0.336 RKM-2018-018 (RSP11110)
  13. 0.333 The Gift (RSP10988)
  14. 0.329 Blueberry Cheesecake (RSP10672)
  15. 0.328 Pie Hoe (RSP11073)
  16. 0.328 CST (RSP11002)
  17. 0.326 RKM-2018-023 (RSP11115)
  18. 0.326 Sour Raspberry (RSP10551)
  19. 0.322 Cbot-2019-005 (RSP11133)
  20. 0.321 KYRG-11 (RSP11051)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448805
Overlapping SNPs:
13
Concordance:
11

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495167
Overlapping SNPs:
2
Concordance:
2
QR code for SRR14708234

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