PP9

SRR 14708260

Grower: Lanzhou University, Guangpeng Ren

General Information

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: Common
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: 1.06%
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: 0.0189
male female SRR14708260

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.749C>A p.Ala250Asp missense variant moderate contig741 4417079

IGV: Start, Jump

G/T
NGS:
0.127
C90:
0.632

Variants (Select Genes of Interest)

GPPs1

UniProt

c.115G>T p.Val39Phe missense variant moderate contig676 168364

IGV: Start, Jump

G/T
NGS:
0.000
C90:
0.000
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
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
ELF3

UniProt

c.520A>C p.Asn174His missense variant moderate contig97 242226

IGV: Start, Jump

A/C
NGS:
0.094
C90:
0.502
ELF3

UniProt

c.772A>G p.Ser258Gly missense variant moderate contig97 242478

IGV: Start, Jump

A/G
NGS:
0.112
C90:
0.000
ELF3

UniProt

c.812G>C p.Gly271Ala missense variant moderate contig97 242518

IGV: Start, Jump

G/C
NGS:
0.114
C90:
0.938
ELF3

UniProt

c.1230-2_1230-1delAG splice acceptor variant & intron variant high contig97 243676

IGV: Start, Jump

TAG/T
NGS:
0.088
C90:
0.450
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.1803_1805delTCA p.His601del disruptive inframe deletion moderate contig97 244625

IGV: Start, Jump

ACAT/A
NGS:
0.092
C90:
0.000
ELF3

UniProt

c.1966C>G p.Pro656Ala missense variant moderate contig97 244797

IGV: Start, Jump

C/G
NGS:
0.123
C90:
0.632
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.629C>T p.Thr210Ile missense variant moderate contig121 2840237

IGV: Start, Jump

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

UniProt

c.331A>G p.Asn111Asp missense variant moderate contig81 209293

IGV: Start, Jump

A/G
NGS:
0.123
C90:
0.000
AAE1-2

UniProt

c.688G>A p.Asp230Asn missense variant moderate contig81 209650

IGV: Start, Jump

G/A
NGS:
0.018
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
PHL-1

UniProt

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

IGV: Start, Jump

T/C
NGS:
0.107
C90:
0.904
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
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.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.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.302A>G p.Asn101Ser missense variant moderate contig121 2829099

IGV: Start, Jump

A/G
NGS:
0.349
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
FLD

UniProt

c.2981T>C p.Met994Thr missense variant moderate contig1450 2044012

IGV: Start, Jump

A/G
NGS:
0.064
C90:
0.478
FLD

UniProt

c.2964C>A p.Asp988Glu missense variant moderate contig1450 2044029

IGV: Start, Jump

G/T
NGS:
0.057
C90:
0.464
AAE1-3

UniProt

c.8C>T p.Ser3Leu missense variant moderate contig976 1084067

IGV: Start, Jump

G/A
NGS:
0.000
C90:
0.000
PKSB-3

UniProt

c.1652A>G p.Glu551Gly missense variant moderate contig93 3339759

IGV: Start, Jump

A/G
NGS:
0.088
C90:
0.000
PKSB-3

UniProt

c.1850_1852dupTGA p.Met617dup disruptive inframe insertion moderate contig93 3339945

IGV: Start, Jump

A/AGAT
NGS:
0.031
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.033 0.067 0.100 0.133
clone distance sibling distance more distant
  1. 0.088 Durban Poison 1 (RSP10996)
  2. 0.088 Super Blue Dream (RSP11011)
  3. 0.094 AOAC MI 535 (RSP11754)
  4. 0.096 Durban Poison 1 (RSP11013)
  5. 0.098 AOAC MI 508 (RSP11750)
  6. 0.102 AOAC MI 588 (RSP11760)
  7. 0.104 Lift (RSP11378)
  8. 0.105 AOAC MI 542 (RSP11755)
  9. 0.105 Liberty Haze (RSP11000)
  10. 0.105 AOAC MI 545 (RSP11756)
  11. 0.106 AOAC MI 533 (RSP11753)
  12. 0.107 AOAC MI 501 (RSP11748)
  13. 0.107 AOAC MI 532 (RSP11752)
  14. 0.107 AOAC MI 597 (RSP11761)
  15. 0.109 Erez (RSP10942)
  16. 0.110 AOAC MI 567 (RSP11758)
  17. 0.111 Suver Haze (RSP11364)
  18. 0.112 AOAC MI 569 (RSP11759)
  19. 0.113 UP Sunrise (RSP10989)
  20. 0.115 AOAC MI 599 (RSP11762)

Nearest genetic relatives (Base Tree)

0 0.067 0.133 0.200 0.267
clone distance sibling distance more distant
  1. 0.132 Liberty Haze (RSP11000)
  2. 0.146 UP Sunrise (RSP10989)
  3. 0.180 Golden Goat 2 (RSP10991)
  4. 0.192 Durban Poison (RSP11014)
  5. 0.194 Blueberry Cheesecake (RSP10684)
  6. 0.200 KYRG-11 (RSP11051)
  7. 0.205 RKM-2018-019 (RSP11111)
  8. 0.209 RKM-2018-022 (RSP11114)
  9. 0.213 RKM-2018-027 (RSP11119)
  10. 0.215 Gold Cracker (RSP11048)
  11. 0.218 RKM-2018-003 (RSP11094)
  12. 0.219 Recon (RSP10755)
  13. 0.219 Pie Hoe (RSP11073)
  14. 0.224 Italian Kiss (RSP11034)
  15. 0.229 Hermaphrodite ResearchSample2 (RSP11050)
  16. 0.231 RKM-2018-032 (RSP11124)
  17. 0.231 RKM-2018-009 (RSP11100)
  18. 0.234 Blueberry Cheesecake (RSP10680)
  19. 0.234 RKM-2018-020 (RSP11112)
  20. 0.236 Blue Dream (RSP11033)

Most genetically distant strains (All Samples)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.417 R1in136 (SRR14708226)
  2. 0.417 80E (RSP11213)
  3. 0.409 CS (RSP11208)
  4. 0.407 Tanao Sri-white 80 (RSP11621)
  5. 0.405 Feral (RSP11205)
  6. 0.400 Cherry Blossom (RSP11323)
  7. 0.385 Santhica27 (RSP11046)
  8. 0.382 80E (RSP11211)
  9. 0.382 Ivory (RSP10668)
  10. 0.378 Tiger Tail 30 (RSP11484)
  11. 0.375 Carmaleonte (RSP11207)
  12. 0.373 Santhica 27 (RSP10665)
  13. 0.371 Tanao Sri 46 (RSP11486)
  14. 0.369 Feral (RSP11206)
  15. 0.366 Santhica27 (RSP11047)
  16. 0.365 JL 4th Gen 5 (RSP11199)
  17. 0.363 JL 3rd Gen Father (RSP11196)
  18. 0.362 JL yellow (RSP11075)
  19. 0.360 USO 31 (RSP10983)
  20. 0.355 Carmagnola (RSP11037)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.372 Carmagnola (RSP10979)
  2. 0.363 Ivory (RSP10668)
  3. 0.359 Carmagnola (RSP11037)
  4. 0.355 Santhica27 (RSP11047)
  5. 0.341 Feral (RSP10890)
  6. 0.323 JL yellow (RSP11075)
  7. 0.320 Skywalker OG (RSP10837)
  8. 0.320 Cbot-2019-005 (RSP11133)
  9. 0.320 Kush Hemp E1 (RSP11128)
  10. 0.316 Tisza (RSP11044)
  11. 0.315 Fedora 17 (RSP10661)
  12. 0.313 Lovrin (RSP10658)
  13. 0.312 Monoica (RSP10241)
  14. 0.306 USO 31 (RSP10981)
  15. 0.302 RKM-2018-026 (RSP11118)
  16. 0.300 Jiangji (RSP10653)
  17. 0.296 RKM-2018-033 (RSP11125)
  18. 0.296 Cbot-2019-001 (RSP11129)
  19. 0.295 Skunk 18 (RSP11038)
  20. 0.295 RKM-2018-034 (RSP11126)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448519
Overlapping SNPs:
16
Concordance:
14

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495189
Overlapping SNPs:
5
Concordance:
5
QR code for SRR14708260

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