Advanced Strain Search

R3in134

SRR 14708219

Grower: Lanzhou University, Guangpeng Ren

General Information

Sample Name
NEB3
Accession Date
May 31, 2021
Reported Plant Sex
unknown

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 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: 1.51%
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: 0.0611
male female SRR14708219

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.845_848delAAAG p.Glu282fs frameshift variant high contig676 169629

IGV: Start, Jump

TGAAA/T
NGS:
0.118
C90:
0.000
GPPs1

UniProt

c.865T>G p.Leu289Val missense variant moderate contig676 169655

IGV: Start, Jump

T/G
NGS:
0.000
C90:
0.000
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.280T>C p.Phe94Leu missense variant moderate contig2621 338845

IGV: Start, Jump

T/C
NGS:
0.000
C90:
0.000
PHL-2 c.722G>A p.Gly241Glu missense variant moderate contig2621 339860

IGV: Start, Jump

G/A
NGS:
0.002
C90:
0.000
PHL-2 c.3202A>C p.Thr1068Pro missense variant moderate contig2621 343245

IGV: Start, Jump

A/C
NGS:
0.053
C90:
0.000
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.3494C>G p.Ser1165Trp missense variant moderate contig2621 343537

IGV: Start, Jump

C/G
NGS:
0.000
C90:
0.000
PKSG-4b

UniProt

c.554A>G p.Tyr185Cys missense variant moderate contig700 2721119

IGV: Start, Jump

T/C
NGS:
0.004
C90:
0.000
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.431T>G p.Val144Gly missense variant moderate contig700 2721242

IGV: Start, Jump

A/C
NGS:
0.575
C90:
0.679
PKSG-4b

UniProt

c.352_355delACAG p.Thr118fs frameshift variant high contig700 2721317

IGV: Start, Jump

CCTGT/C
NGS:
0.529
C90:
0.000
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
PKSG-4b

UniProt

c.323A>G p.Glu108Gly missense variant moderate contig700 2721350

IGV: Start, Jump

T/C
NGS:
0.469
C90:
0.000
PKSG-4a

UniProt

c.1191_1193delTTA p.Tyr398del disruptive inframe deletion moderate contig700 1938600

IGV: Start, Jump

AATT/A
NGS:
0.167
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
OAC-2

UniProt

c.102_103insGATC p.Pro35fs frameshift variant high contig931 110236

IGV: Start, Jump

G/GGATC
NGS:
0.000
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.1366T>G p.Leu456Val missense variant moderate contig97 244197

IGV: Start, Jump

T/G
NGS:
0.015
C90:
0.000
ELF3

UniProt

c.1385C>T p.Ala462Val missense variant moderate contig97 244216

IGV: Start, Jump

C/T
NGS:
0.004
C90:
0.000
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
ELF3

UniProt

c.1832A>G p.Tyr611Cys missense variant moderate contig97 244663

IGV: Start, Jump

A/G
NGS:
0.004
C90:
0.000
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.715G>C p.Ala239Pro missense variant moderate contig121 2841350

IGV: Start, Jump

G/C
NGS:
0.004
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.936A>C p.Leu312Phe missense variant moderate contig121 2842582

IGV: Start, Jump

A/C
NGS:
0.000
C90:
0.000
aPT1

UniProt

c.938C>T p.Thr313Ile missense variant moderate contig121 2842584

IGV: Start, Jump

C/T
NGS:
0.000
C90:
0.000
aPT1

UniProt

c.958G>A p.Gly320Ser missense variant moderate contig121 2842731

IGV: Start, Jump

G/A
NGS:
0.004
C90:
0.000
AAE1-2

UniProt

c.1006A>G p.Lys336Glu missense variant moderate contig81 209968

IGV: Start, Jump

A/G
NGS:
0.116
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
PHL-1

UniProt

c.2813C>A p.Pro938Gln missense variant moderate contig1439 1486984

IGV: Start, Jump

G/T
NGS:
0.000
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
PHL-1

UniProt

c.2551A>G p.Thr851Ala missense variant moderate contig1439 1487246

IGV: Start, Jump

T/C
NGS:
0.116
C90:
0.890
PHL-1

UniProt

c.1387A>G p.Thr463Ala missense variant moderate contig1439 1489811

IGV: Start, Jump

T/C
NGS:
0.107
C90:
0.904
PHL-1

UniProt

c.919A>G p.Ser307Gly missense variant moderate contig1439 1490279

IGV: Start, Jump

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

UniProt

c.317C>T p.Thr106Met missense variant moderate contig1439 1492393

IGV: Start, Jump

G/A
NGS:
0.000
C90:
0.000
Edestin

UniProt

c.16T>G p.Ser6Ala missense variant moderate contig850 3065274

IGV: Start, Jump

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

UniProt

c.-5_1delATAATA p.Met1del start lost & conservative inframe deletion high contig700 1951880

IGV: Start, Jump

ATATTAT/A
NGS:
0.007
C90:
0.000
TFL1

UniProt

c.302-1G>A splice acceptor variant & intron variant high contig1636 520616

IGV: Start, Jump

C/T
NGS:
0.103
C90:
0.794
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.1378G>A p.Val460Ile missense variant moderate contig1891 886370

IGV: Start, Jump

C/T
NGS:
0.167
C90:
0.000
HDS-1

UniProt

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

IGV: Start, Jump

C/T
NGS:
0.088
C90:
0.593
HDS-1

UniProt

c.-108+1_-108+2insG splice donor variant & intron variant high contig1891 889975

IGV: Start, Jump

A/AC
NGS:
0.217
C90:
0.000
PIE1-2

UniProt

c.1289A>G p.Asp430Gly missense variant moderate contig1460 1192109

IGV: Start, Jump

T/C
NGS:
0.079
C90:
0.000
EMF2

UniProt

c.1772A>G p.Gln591Arg missense variant moderate contig954 3059929

IGV: Start, Jump

A/G
NGS:
0.092
C90:
0.876
aPT4

UniProt

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

IGV: Start, Jump

G/A
NGS:
0.158
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.355A>T p.Ile119Phe missense variant moderate contig121 2829152

IGV: Start, Jump

A/T
NGS:
0.000
C90:
0.000
aPT4

UniProt

c.916C>T p.His306Tyr missense variant & splice region variant moderate contig121 2832711

IGV: Start, Jump

C/T
NGS:
0.015
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
FLD

UniProt

c.2869C>T p.His957Tyr missense variant moderate contig1450 2044163

IGV: Start, Jump

G/A
NGS:
0.011
C90:
0.000
AAE1-3

UniProt

c.167A>G p.Glu56Gly missense variant moderate contig976 1083908

IGV: Start, Jump

T/C
NGS:
0.070
C90:
0.000
AAE1-3

UniProt

c.118G>A p.Ala40Thr missense variant moderate contig976 1083957

IGV: Start, Jump

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

UniProt

c.53G>T p.Gly18Val missense variant moderate contig976 1084022

IGV: Start, Jump

C/A
NGS:
0.000
C90:
0.000
GGR

UniProt

c.317C>T p.Pro106Leu missense variant moderate contig2282 549309

IGV: Start, Jump

C/T
NGS:
0.035
C90:
0.220
GGR

UniProt

c.376G>C p.Glu126Gln missense variant moderate contig2282 549368

IGV: Start, Jump

G/C
NGS:
0.015
C90:
0.110
GGR

UniProt

c.382C>T p.Leu128Phe missense variant moderate contig2282 549374

IGV: Start, Jump

C/T
NGS:
0.024
C90:
0.000
GGR

UniProt

c.704A>T p.His235Leu missense variant moderate contig2282 549696

IGV: Start, Jump

A/T
NGS:
0.121
C90:
0.000
PKSB-3

UniProt

c.25C>T p.His9Tyr missense variant moderate contig93 3333316

IGV: Start, Jump

C/T
NGS:
0.000
C90:
0.000

Nearest genetic relatives (All Samples)

clone distance sibling distance more distant
  1. 0.175 KYRG-11 (RSP11051)
  2. 0.176 R3in134 (SRR14708220)
  3. 0.183 R3in134 (SRR14708235)
  4. 0.191 UnObtanium (RSP11611)
  5. 0.199 R2in135 (SRR14708236)
  6. 0.205 QHI (SRR14708202)
  7. 0.207 Mexican Sativa (SRR14708263)
  8. 0.208 B52 (SRR14708255)
  9. 0.212 R3in134 (SRR14708218)
  10. 0.217 Electra (RSP11366)
  11. 0.221 AOAC MI 567 (RSP11758)
  12. 0.221 AOAC MI 597 (RSP11761)
  13. 0.229 VIR 469 (SRR14708242)
  14. 0.230 AOAC MI 501 (RSP11748)
  15. 0.230 PEU (SRR14708215)
  16. 0.231 Lift (RSP11378)
  17. 0.232 XUM2 (SRR14708204)
  18. 0.233 AOAC MI 542 (RSP11755)
  19. 0.234 Cherry Gar-See-Ya (RSP11642)
  20. 0.235 AOAC MI 533 (RSP11753)

Nearest genetic relatives (Base Tree)

clone distance sibling distance more distant
  1. 0.203 KYRG-11 (RSP11051)
  2. 0.205 Blueberry Cheesecake (RSP10684)
  3. 0.236 Liberty Haze (RSP11000)
  4. 0.250 Jiangji (RSP10653)
  5. 0.253 USO 31 (RSP10981)
  6. 0.279 Gold Cracker (RSP11048)
  7. 0.280 RKM-2018-020 (RSP11112)
  8. 0.282 RKM-2018-005 (RSP11096)
  9. 0.283 RKM-2018-019 (RSP11111)
  10. 0.284 Durban Poison (RSP11014)
  11. 0.285 Pie Hoe (RSP11073)
  12. 0.291 UP Sunrise (RSP10989)
  13. 0.295 Skywalker OG (RSP10837)
  14. 0.296 Cbot-2019-006 (RSP11134)
  15. 0.298 RKM-2018-018 (RSP11110)
  16. 0.302 Tygra (RSP10667)
  17. 0.306 RKM-2018-027 (RSP11119)
  18. 0.306 Tisza (RSP11044)
  19. 0.307 Golden Goat 2 (RSP10991)
  20. 0.309 Blue Dream (RSP11033)

Most genetically distant strains (All Samples)

clone distance sibling distance more distant
  1. 0.460 JL yellow (RSP11075)
  2. 0.449 JL 4th Gen 3 (RSP11195)
  3. 0.448 JL 4th Gen 5 (RSP11199)
  4. 0.446 Chematonic Cannatonic x Chemdawg (RSP11394)
  5. 0.443 JL 3rd Gen Mother (RSP11214)
  6. 0.440 JL 4th Gen 1 (RSP11193)
  7. 0.422 JL 4th Gen 4 (RSP11198)
  8. 0.415 JL 3rd Gen Father (RSP11196)
  9. 0.412 Cherry Blossom (RSP11301)
  10. 0.412 JL 4th Gen 2 (RSP11194)
  11. 0.405 Wife (RSP11148)
  12. 0.404 Cherry Blossom (RSP11298)
  13. 0.403 Cherry Blossom (RSP11309)
  14. 0.400 JL 3rd Gen Mother (RSP11197)
  15. 0.397 80E (RSP11213)
  16. 0.394 Feral (RSP11206)
  17. 0.392 JL 2 (RSP11076)
  18. 0.391 80E (RSP11211)
  19. 0.385 Tanao Sri 46 (RSP11486)
  20. 0.384 Northern Lights (RSP11501)

Most genetically distant strains (Base Tree)

clone distance sibling distance more distant
  1. 0.473 JL yellow (RSP11075)
  2. 0.388 RKM-2018-006 (RSP11097)
  3. 0.383 Ivory (RSP10668)
  4. 0.380 Sour Raspberry (RSP10551)
  5. 0.373 Skunk 18 (RSP11038)
  6. 0.373 RKM-2018-003 (RSP11094)
  7. 0.371 Cbot-2019-004 (RSP11132)
  8. 0.364 Santhica27 (RSP11047)
  9. 0.362 CST (RSP11002)
  10. 0.358 Blueberry Cheesecake (RSP10672)
  11. 0.357 Cherry (RSP11142)
  12. 0.355 Cbot-2019-005 (RSP11133)
  13. 0.354 Cbot-2019-001 (RSP11129)
  14. 0.352 Italian Kiss (RSP11034)
  15. 0.352 RKM-2018-028 (RSP11120)
  16. 0.348 Tisza (RSP10659)
  17. 0.346 RKM-2018-033 (RSP11125)
  18. 0.344 Black Beauty (RSP11035)
  19. 0.341 Feral (RSP10890)
  20. 0.341 Kimbo Slice (RSP10997)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448524
Overlapping SNPs:
12
Concordance:
11

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495174
Overlapping SNPs:
3
Concordance:
2
QR code for SRR14708219

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