R2in135

SRR 14708224

Grower: Lanzhou University, Guangpeng Ren

General Information

Sample Name
NER2
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 I

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: 1.55%
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: 0.0631
male female SRR14708224

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.373G>C p.Val125Leu missense variant moderate contig741 4417455

IGV: Start, Jump

C/G
NGS:
0.050
C90:
0.000

Variants (Select Genes of Interest)

GPPs1

UniProt

c.744C>G p.Asp248Glu missense variant moderate contig676 168993

IGV: Start, Jump

C/G
NGS:
0.022
C90:
0.000
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.885+1G>T splice donor variant & intron variant high contig676 169676

IGV: Start, Jump

G/T
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
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.520A>C p.Asn174His missense variant moderate contig97 242226

IGV: Start, Jump

A/C
NGS:
0.094
C90:
0.502
ELF5

UniProt

c.365A>G p.Lys122Arg missense variant moderate contig382 880053

IGV: Start, Jump

A/G
NGS:
0.000
C90:
0.000
ELF5

UniProt

c.1312C>A p.Pro438Thr missense variant moderate contig382 881282

IGV: Start, Jump

C/A
NGS:
0.000
C90:
0.000
ELF5

UniProt

c.1313C>T p.Pro438Leu missense variant moderate contig382 881283

IGV: Start, Jump

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

UniProt

c.22G>A p.Val8Ile missense variant moderate contig931 118442

IGV: Start, Jump

C/T
NGS:
0.004
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
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
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.-108+1_-108+2insG splice donor variant & intron variant high contig1891 889975

IGV: Start, Jump

A/AC
NGS:
0.217
C90:
0.000
EMF2

UniProt

c.434C>T p.Ser145Phe missense variant moderate contig954 3049270

IGV: Start, Jump

C/T
NGS:
0.018
C90:
0.057
EMF2

UniProt

c.722C>T p.Thr241Ile missense variant moderate contig954 3050302

IGV: Start, Jump

C/T
NGS:
0.018
C90:
0.062
EMF2

UniProt

c.1183G>A p.Glu395Lys missense variant moderate contig954 3054195

IGV: Start, Jump

G/A
NGS:
0.009
C90:
0.000
EMF2

UniProt

c.1315G>C p.Ala439Pro missense variant moderate contig954 3055804

IGV: Start, Jump

G/C
NGS:
0.015
C90:
0.053
EMF2

UniProt

c.1742C>G p.Thr581Ser missense variant moderate contig954 3059899

IGV: Start, Jump

C/G
NGS:
0.011
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
FT

UniProt

c.240C>G p.Asn80Lys missense variant moderate contig1561 3124664

IGV: Start, Jump

C/G
NGS:
0.075
C90:
0.000
FT

UniProt

c.413_413+1insGTATGCA splice donor variant & intron variant high contig1561 3126450

IGV: Start, Jump

T/TGTATGCA
NGS:
0.007
C90:
0.000
FT

UniProt

c.419G>A p.Ser140Asn missense variant moderate contig1561 3126658

IGV: Start, Jump

G/A
NGS:
0.013
C90:
0.033
FT

UniProt

c.421_422dupTA p.Leu142fs frameshift variant high contig1561 3126659

IGV: Start, Jump

C/CTA
NGS:
0.000
C90:
0.000
FT

UniProt

c.424C>A p.Leu142Ile missense variant moderate contig1561 3126663

IGV: Start, Jump

C/A
NGS:
0.000
C90:
0.000
FT

UniProt

c.440A>C p.Ter147Serext*? stop lost & splice region variant high contig1561 3126679

IGV: Start, Jump

A/C
NGS:
0.013
C90:
0.038
aPT4

UniProt

c.202T>A p.Leu68Ile missense variant moderate contig121 2828858

IGV: Start, Jump

T/A
NGS:
0.068
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.450G>A p.Met150Ile missense variant moderate contig121 2830645

IGV: Start, Jump

G/A
NGS:
0.007
C90:
0.000
FLD

UniProt

c.2686G>A p.Ala896Thr missense variant moderate contig1450 2044848

IGV: Start, Jump

C/T
NGS:
0.035
C90:
0.225
FLD

UniProt

c.2681T>C p.Ile894Thr missense variant moderate contig1450 2044853

IGV: Start, Jump

A/G
NGS:
0.020
C90:
0.144
FLD

UniProt

c.2598-2_2598-1insA splice acceptor variant & intron variant high contig1450 2044937

IGV: Start, Jump

C/CT
NGS:
0.002
C90:
0.000
AAE1-3

UniProt

c.416T>C p.Leu139Pro missense variant moderate contig976 1083609

IGV: Start, Jump

A/G
NGS:
0.061
C90:
0.000
AAE1-3

UniProt

c.224C>T p.Pro75Leu missense variant moderate contig976 1083851

IGV: Start, Jump

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

UniProt

c.208G>C p.Ala70Pro missense variant moderate contig976 1083867

IGV: Start, Jump

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

UniProt

c.199A>G p.Asn67Asp missense variant moderate contig976 1083876

IGV: Start, Jump

T/C
NGS:
0.079
C90:
0.000
AAE1-3

UniProt

c.188A>G p.Asn63Ser missense variant moderate contig976 1083887

IGV: Start, Jump

T/C
NGS:
0.077
C90:
0.000
AAE1-3

UniProt

c.79A>G p.Thr27Ala missense variant moderate contig976 1083996

IGV: Start, Jump

T/C
NGS:
0.068
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.317C>T p.Pro106Leu missense variant moderate contig2282 549309

IGV: Start, Jump

C/T
NGS:
0.035
C90:
0.220
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
GGR

UniProt

c.581C>T p.Ala194Val missense variant moderate contig2282 549573

IGV: Start, Jump

C/T
NGS:
0.015
C90:
0.105
GGR

UniProt

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

IGV: Start, Jump

A/T
NGS:
0.121
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.050 0.100 0.150 0.200
clone distance sibling distance more distant
  1. 0.149 AOAC MI 535 (RSP11754)
  2. 0.155 AOAC MI 504 (RSP11749)
  3. 0.159 AOAC MI 508 (RSP11750)
  4. 0.159 B52 (SRR14708255)
  5. 0.161 AOAC MI 545 (RSP11756)
  6. 0.163 AOAC MI 533 (RSP11753)
  7. 0.163 AOAC MI 599 (RSP11762)
  8. 0.164 Serious Happiness (RSP10763)
  9. 0.165 AOAC MI 567 (RSP11758)
  10. 0.167 Durban Poison 1 (RSP11013)
  11. 0.169 AOAC MI 501 (RSP11748)
  12. 0.169 Liberty Haze (RSP11000)
  13. 0.170 AOAC MI 532 (RSP11752)
  14. 0.172 AOAC MI 588 (RSP11760)
  15. 0.172 AOAC MI 542 (RSP11755)
  16. 0.172 AOAC MI 597 (RSP11761)
  17. 0.176 AOAC MI 569 (RSP11759)
  18. 0.177 AOAC MI 548 (RSP11757)
  19. 0.185 Blue Dream (RSP11007)
  20. 0.186 Electra (RSP11366)

Nearest genetic relatives (Base Tree)

0 0.075 0.150 0.225 0.300
clone distance sibling distance more distant
  1. 0.170 Liberty Haze (RSP11000)
  2. 0.207 Blueberry Cheesecake (RSP10684)
  3. 0.213 KYRG-11 (RSP11051)
  4. 0.230 Lovrin (RSP10658)
  5. 0.239 UP Sunrise (RSP10989)
  6. 0.244 Italian Kiss (RSP11034)
  7. 0.246 RKM-2018-005 (RSP11096)
  8. 0.250 The Gift (RSP10988)
  9. 0.250 Hermaphrodite ResearchSample2 (RSP11050)
  10. 0.256 Golden Goat 2 (RSP10991)
  11. 0.259 USO 31 (RSP10981)
  12. 0.261 Kyrgyz Gold (RSP11054)
  13. 0.261 Ivory (RSP10668)
  14. 0.262 RKM-2018-033 (RSP11125)
  15. 0.263 RKM-2018-009 (RSP11100)
  16. 0.264 RKM-2018-029 (RSP11121)
  17. 0.265 Gold Cracker (RSP11048)
  18. 0.269 Futura 75 (RSP10664)
  19. 0.270 QUEEN JESUS (RSP10105)
  20. 0.271 Kimbo Slice (RSP10997)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.449 80E (RSP11213)
  2. 0.436 JL yellow (RSP11075)
  3. 0.431 JL 4th Gen 5 (RSP11199)
  4. 0.413 80E (RSP11212)
  5. 0.413 JL 4th Gen 2 (RSP11194)
  6. 0.403 JL 4th Gen 6 (RSP11200)
  7. 0.401 JL 4th Gen 1 (RSP11193)
  8. 0.399 JL 4th Gen 4 (RSP11198)
  9. 0.398 JL 3rd Gen Father (RSP11196)
  10. 0.394 Feral (RSP11205)
  11. 0.394 Chematonic Cannatonic x Chemdawg (RSP11394)
  12. 0.389 Cbot-2019-005 (RSP11133)
  13. 0.386 JL 3rd Gen Mother (RSP11214)
  14. 0.385 JL 3rd Gen Mother (RSP11197)
  15. 0.383 Tanao Sri 46 (RSP11486)
  16. 0.383 IUP3 (SRR14708256)
  17. 0.381 IUP2 (SRR14708257)
  18. 0.381 Red Eye OG (RSP11190)
  19. 0.380 Tanao Sri-white 80 (RSP11621)
  20. 0.379 Carmagnola (RSP10979)

Most genetically distant strains (Base Tree)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.425 JL yellow (RSP11075)
  2. 0.392 Carmagnola (RSP10979)
  3. 0.376 RKM-2018-026 (RSP11118)
  4. 0.373 Cbot-2019-005 (RSP11133)
  5. 0.369 Kush Hemp E1 (RSP11128)
  6. 0.366 Skywalker OG (RSP10837)
  7. 0.365 RKM-2018-002 (RSP11093)
  8. 0.352 Feral (RSP10890)
  9. 0.351 Cbot-2019-004 (RSP11132)
  10. 0.347 RKM-2018-022 (RSP11114)
  11. 0.345 RKM-2018-034 (RSP11126)
  12. 0.339 Cherry (RSP11142)
  13. 0.333 Black Beauty (RSP11035)
  14. 0.332 RKM-2018-019 (RSP11111)
  15. 0.329 Cherry (RSP11143)
  16. 0.327 Jiangji (RSP10653)
  17. 0.327 Blueberry Cheesecake (RSP10680)
  18. 0.326 Carmagnola (RSP11037)
  19. 0.324 Durban Poison (RSP11014)
  20. 0.322 Pie Hoe (RSP11073)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448491
Overlapping SNPs:
10
Concordance:
10

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495237
Overlapping SNPs:
5
Concordance:
5
QR code for SRR14708224

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