R1in136

SRR 14708226

Grower: Lanzhou University, Guangpeng Ren

General Information

Sample Name
ERM3
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: 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
Unknown

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: 1.16%
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: 0.0224
male female SRR14708226

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)

CBDAS c.8G>A p.Cys3Tyr missense variant moderate contig1772 2082234

IGV: Start, Jump

G/A
NGS:
0.057
C90:
0.000
CBDAS c.503A>G p.Asn168Ser missense variant moderate contig1772 2082729

IGV: Start, Jump

A/G
NGS:
0.024
C90:
0.062
CBDAS c.587A>G p.Asn196Ser missense variant moderate contig1772 2082813

IGV: Start, Jump

A/G
NGS:
0.011
C90:
0.435
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.845_848delAAAG p.Glu282fs frameshift variant high contig676 169629

IGV: Start, Jump

TGAAA/T
NGS:
0.118
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
EMF1-2

UniProt

c.1187T>C p.Leu396Ser missense variant moderate contig885 2073

IGV: Start, Jump

T/C
NGS:
0.026
C90:
0.000
PHL-2 c.1057A>G p.Arg353Gly missense variant moderate contig2621 340335

IGV: Start, Jump

A/G
NGS:
0.096
C90:
0.555
PHL-2 c.2564T>A p.Phe855Tyr missense variant moderate contig2621 342607

IGV: Start, Jump

T/A
NGS:
0.064
C90:
0.732
PHL-2 c.2578T>A p.Leu860Ile missense variant moderate contig2621 342621

IGV: Start, Jump

T/A
NGS:
0.068
C90:
0.746
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.2830A>G p.Asn944Asp missense variant moderate contig2621 342873

IGV: Start, Jump

A/G
NGS:
0.018
C90:
0.000
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.3467A>G p.Gln1156Arg missense variant moderate contig2621 343510

IGV: Start, Jump

A/G
NGS:
0.064
C90:
0.713
PKSG-4a

UniProt

c.261_264dupGTAC p.Met89fs frameshift variant high contig700 1937671

IGV: Start, Jump

A/AGTAC
NGS:
0.004
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
OAC-2

UniProt

c.185C>T p.Thr62Ile missense variant moderate contig931 110054

IGV: Start, Jump

G/A
NGS:
0.029
C90:
0.000
OAC-2

UniProt

c.22G>A p.Val8Ile missense variant moderate contig931 110317

IGV: Start, Jump

C/T
NGS:
0.018
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.1435G>C p.Ala479Pro missense variant moderate contig97 244266

IGV: Start, Jump

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

IGV: Start, Jump

C/G
NGS:
0.123
C90:
0.632
ELF3

UniProt

c.2198G>T p.Arg733Leu missense variant moderate contig97 245029

IGV: Start, Jump

G/T
NGS:
0.125
C90:
0.531
aPT1

UniProt

c.406A>G p.Ile136Val missense variant moderate contig121 2839605

IGV: Start, Jump

A/G
NGS:
0.579
C90:
0.761
HDS-2

UniProt

c.679G>C p.Gly227Arg missense variant moderate contig95 1990632

IGV: Start, Jump

G/C
NGS:
0.037
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.2623A>G p.Thr875Ala missense variant moderate contig1439 1487174

IGV: Start, Jump

T/C
NGS:
0.123
C90:
0.000
Edestin

UniProt

c.271_272insTCA p.Leu90_Arg91insIle conservative inframe insertion moderate contig850 3065018

IGV: Start, Jump

C/CTGA
NGS:
0.000
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.1378G>A p.Val460Ile missense variant moderate contig1891 886370

IGV: Start, Jump

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

UniProt

c.56C>G p.Ala19Gly missense variant moderate contig1891 889336

IGV: Start, Jump

G/C
NGS:
0.125
C90:
0.943
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.1772A>G p.Gln591Arg missense variant moderate contig954 3059929

IGV: Start, Jump

A/G
NGS:
0.092
C90:
0.876
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.517A>T p.Ile173Leu missense variant & splice region variant moderate contig121 2830795

IGV: Start, Jump

A/T
NGS:
0.022
C90:
0.000
FLD

UniProt

c.2811_2813dupGGG p.Gly938dup disruptive inframe insertion & splice region variant moderate contig1450 2044218

IGV: Start, Jump

T/TCCC
NGS:
0.000
C90:
0.000
FLD

UniProt

c.125G>A p.Ser42Asn missense variant moderate contig1450 2047909

IGV: Start, Jump

C/T
NGS:
0.037
C90:
0.388
AAE1-3

UniProt

c.382T>C p.Tyr128His missense variant moderate contig976 1083643

IGV: Start, Jump

A/G
NGS:
0.072
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
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 0.067 0.133 0.200 0.267
clone distance sibling distance more distant
  1. 0.172 USO31 (RSP10233)
  2. 0.198 KYRG-11 (RSP11051)
  3. 0.204 R1in136 (SRR14708227)
  4. 0.210 USO 31 (RSP10981)
  5. 0.211 USO 31 (RSP10983)
  6. 0.213 R1in136 (SRR14708225)
  7. 0.216 Juso14 (SRR14708259)
  8. 0.224 Futura 75 (RSP10664)
  9. 0.229 Kompolti (SRR14708277)
  10. 0.233 VIR 483 (SRR14708239)
  11. 0.235 XUM2 (SRR14708204)
  12. 0.235 Santhica 27 (SRR14708211)
  13. 0.238 R1in136 (SRR14708237)
  14. 0.240 VIR 223, Bernburgskaya Odnodomnaya, bm (SRR14708217)
  15. 0.240 Bialobrzeskie (SRR14708244)
  16. 0.246 XUM1 (SRR14708205)
  17. 0.252 VIR 507, Krasnodarsky 10 FB (SRR14708229)
  18. 0.254 KYRG-151 (RSP11052)
  19. 0.254 VIR 483 (SRR14708240)
  20. 0.257 VIR 369 (SRR14708231)

Nearest genetic relatives (Base Tree)

0 0.083 0.167 0.250 0.333
clone distance sibling distance more distant
  1. 0.228 Futura 75 (RSP10664)
  2. 0.231 USO 31 (RSP10981)
  3. 0.232 KYRG-11 (RSP11051)
  4. 0.264 UP Sunrise (RSP10989)
  5. 0.270 Santhica27 (RSP11047)
  6. 0.277 Lovrin (RSP10658)
  7. 0.286 Fedora 17 (RSP10661)
  8. 0.286 Blueberry Cheesecake (RSP10684)
  9. 0.288 Tisza (RSP10659)
  10. 0.292 Liberty Haze (RSP11000)
  11. 0.298 Monoica (RSP10241)
  12. 0.307 Tygra (RSP10667)
  13. 0.310 Tisza (RSP11044)
  14. 0.312 Hermaphrodite Research Sample1 (RSP11049)
  15. 0.317 Ivory (RSP10668)
  16. 0.322 RKM-2018-028 (RSP11120)
  17. 0.324 The Gift (RSP10988)
  18. 0.324 RKM-2018-018 (RSP11110)
  19. 0.327 Skunk 18 (RSP11038)
  20. 0.333 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. 0.481 JL 4th Gen 6 (RSP11200)
  2. 0.479 JL 3rd Gen Mother (RSP11197)
  3. 0.470 JL yellow (RSP11075)
  4. 0.463 Cherry Blossom (RSP11312)
  5. 0.463 UP Sunset (RSP11256)
  6. 0.463 JL 4th Gen 3 (RSP11195)
  7. 0.458 Cherry Blossom (RSP11274)
  8. 0.456 Chematonic Cannatonic x Chemdawg (RSP11394)
  9. 0.449 Northern Lights (RSP11501)
  10. 0.444 JL 4th Gen 5 (RSP11199)
  11. 0.441 Chem 91 (RSP11185)
  12. 0.436 Candy Kush (RSP11492)
  13. 0.436 Cherry Blossom (RSP11298)
  14. 0.434 Grape Stomper (RSP11180)
  15. 0.434 JL 3rd Gen Mother (RSP11214)
  16. 0.434 Wife (RSP11148)
  17. 0.433 Cbot-2019-004 (RSP11132)
  18. 0.433 Danny Noonan (RSP11070)
  19. 0.430 Cbot-2019-003 (RSP11131)
  20. 0.428 Unknown- Cherry Wine - 003 (RSP11270)

Most genetically distant strains (Base Tree)

0 0.125 0.250 0.375 0.500
clone distance sibling distance more distant
  1. 0.470 JL yellow (RSP11075)
  2. 0.425 Cbot-2019-004 (RSP11132)
  3. 0.420 CST (RSP11002)
  4. 0.412 Blueberry Cheesecake (RSP10672)
  5. 0.412 RKM-2018-019 (RSP11111)
  6. 0.408 Cbot-2019-005 (RSP11133)
  7. 0.408 RKM-2018-006 (RSP11097)
  8. 0.405 RKM-2018-009 (RSP11100)
  9. 0.402 RKM-2018-022 (RSP11114)
  10. 0.396 Sour Raspberry (RSP10551)
  11. 0.392 Cbot-2019-001 (RSP11129)
  12. 0.391 Kush Hemp E1 (RSP11128)
  13. 0.390 Durban Poison (RSP11014)
  14. 0.388 RKM-2018-020 (RSP11112)
  15. 0.387 RKM-2018-003 (RSP11094)
  16. 0.385 RKM-2018-005 (RSP11096)
  17. 0.385 RKM-2018-002 (RSP11093)
  18. 0.384 RKM-2018-023 (RSP11115)
  19. 0.383 Blueberry Cheesecake (RSP10680)
  20. 0.383 RKM-2018-033 (RSP11125)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4450099
Overlapping SNPs:
10
Concordance:
9

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495321
Overlapping SNPs:
3
Concordance:
2
QR code for SRR14708226

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