Hindu Kush

SRR 14708261

Grower: Lanzhou University, Guangpeng Ren

General Information

Sample Name
HKH
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%
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: 0.0192
male female SRR14708261

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)

EMF1-2

UniProt

c.1384A>C p.Lys462Gln missense variant moderate contig885 2270

IGV: Start, Jump

A/C
NGS:
0.013
C90:
0.254
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.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
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.431T>G p.Val144Gly missense variant moderate contig700 2721242

IGV: Start, Jump

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

UniProt

c.419A>G p.Asp140Gly missense variant moderate contig700 2721254

IGV: Start, Jump

T/C
NGS:
0.430
C90:
0.440
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.323A>G p.Glu108Gly missense variant moderate contig700 2721350

IGV: Start, Jump

T/C
NGS:
0.469
C90:
0.000
PKSG-2a

UniProt

c.67T>A p.Phe23Ile missense variant moderate contig700 1945567

IGV: Start, Jump

A/T
NGS:
0.825
C90:
0.904
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
aPT1

UniProt

c.160A>C p.Thr54Pro missense variant moderate contig121 2835867

IGV: Start, Jump

A/C
NGS:
0.086
C90:
0.048
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.864C>G p.Asn288Lys missense variant moderate contig121 2842407

IGV: Start, Jump

C/G
NGS:
0.075
C90:
0.062
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
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
PKSG-2b

UniProt

c.31A>T p.Thr11Ser missense variant moderate contig700 1951851

IGV: Start, Jump

T/A
NGS:
0.844
C90:
0.880
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.1381G>A p.Asp461Asn missense variant moderate contig1891 886367

IGV: Start, Jump

C/T
NGS:
0.029
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.136G>A p.Val46Ile missense variant moderate contig1891 889256

IGV: Start, Jump

C/T
NGS:
0.088
C90:
0.593
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.35G>A p.Cys12Tyr missense variant moderate contig1891 889357

IGV: Start, Jump

C/T
NGS:
0.094
C90:
0.646
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.153A>C p.Lys51Asn missense variant moderate contig121 2828809

IGV: Start, Jump

A/C
NGS:
0.375
C90:
0.000
aPT4

UniProt

c.198A>C p.Lys66Asn missense variant moderate contig121 2828854

IGV: Start, Jump

A/C
NGS:
0.044
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.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.976_986delGGAATTGTTCT p.Gly326fs frameshift variant high contig121 2832763

IGV: Start, Jump

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

UniProt

c.667G>A p.Val223Ile missense variant moderate contig976 1083187

IGV: Start, Jump

C/T
NGS:
0.048
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.475G>A p.Gly159Arg missense variant moderate contig976 1083550

IGV: Start, Jump

C/T
NGS:
0.048
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.296C>T p.Pro99Leu missense variant moderate contig976 1083729

IGV: Start, Jump

G/A
NGS:
0.046
C90:
0.000
AAE1-3

UniProt

c.293A>G p.Asp98Gly missense variant moderate contig976 1083732

IGV: Start, Jump

T/C
NGS:
0.068
C90:
0.000
AAE1-3

UniProt

c.284A>T p.Glu95Val missense variant moderate contig976 1083741

IGV: Start, Jump

T/A
NGS:
0.053
C90:
0.000
AAE1-3

UniProt

c.52G>A p.Gly18Ser missense variant moderate contig976 1084023

IGV: Start, Jump

C/T
NGS:
0.064
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 0.042 0.083 0.125 0.167
clone distance sibling distance more distant
  1. 0.081 Blue Dream (RSP11004)
  2. 0.081 Blue Dream (RSP11010)
  3. 0.092 Super Blue Dream (RSP11011)
  4. 0.098 Blue Dream (RSP11009)
  5. 0.103 Blue Dream (RSP11017)
  6. 0.113 Blue Dream (RSP11012)
  7. 0.122 Serious Happiness (RSP10763)
  8. 0.125 Blue Dream (RSP11006)
  9. 0.125 Blue Dream (RSP11007)
  10. 0.129 Blue Dream (RSP11008)
  11. 0.138 Electra (RSP11366)
  12. 0.141 Snoops Dream (RSP11003)
  13. 0.142 Blue Dream (RSP11005)
  14. 0.143 AOAC MI 533 (RSP11753)
  15. 0.144 AOAC MI 508 (RSP11750)
  16. 0.144 Durban Poison 1 (RSP10996)
  17. 0.145 Italian Kiss (RSP10990)
  18. 0.146 AOAC MI 535 (RSP11754)
  19. 0.147 Gold Cracker (RSP11048)
  20. 0.148 AOAC MI 599 (RSP11762)

Nearest genetic relatives (Base Tree)

0 0.058 0.117 0.175 0.233
clone distance sibling distance more distant
  1. 0.130 Italian Kiss (RSP11034)
  2. 0.152 Liberty Haze (RSP11000)
  3. 0.162 Gold Cracker (RSP11048)
  4. 0.171 Blue Dream (RSP11033)
  5. 0.179 UP Sunrise (RSP10989)
  6. 0.182 RKM-2018-006 (RSP11097)
  7. 0.185 RKM-2018-003 (RSP11094)
  8. 0.198 Durban Poison (RSP11014)
  9. 0.199 RKM-2018-009 (RSP11100)
  10. 0.202 RKM-2018-023 (RSP11115)
  11. 0.207 RKM-2018-028 (RSP11120)
  12. 0.213 RKM-2018-018 (RSP11110)
  13. 0.217 QUEEN JESUS (RSP10105)
  14. 0.218 Hermaphrodite Research Sample1 (RSP11049)
  15. 0.218 KYRG-11 (RSP11051)
  16. 0.218 RKM-2018-027 (RSP11119)
  17. 0.219 CST (RSP11002)
  18. 0.227 Tygra (RSP10667)
  19. 0.227 Golden Goat 2 (RSP10991)
  20. 0.227 Skunk 18 (RSP11038)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.454 Feral (RSP11205)
  2. 0.426 80E (RSP11213)
  3. 0.418 Cherry Blossom (RSP11328)
  4. 0.411 Cherry Blossom (RSP11298)
  5. 0.403 Tanao Sri-white 80 (RSP11621)
  6. 0.401 Cherry Blossom (RSP11317)
  7. 0.390 Tanao Sri-white-T1 (RSP11658)
  8. 0.387 SFVxTK (RSP11072)
  9. 0.386 80E (RSP11211)
  10. 0.385 Red Eye OG (RSP11190)
  11. 0.384 Cherry Blossom (RSP11330)
  12. 0.383 IUP3 (SRR14708256)
  13. 0.383 R3in134 (SRR14708218)
  14. 0.382 Bialobrzeskie (SRR14708244)
  15. 0.381 Cherry Blossom (RSP11309)
  16. 0.380 R3in134 (SRR14708235)
  17. 0.379 Cherry Blossom CBG (RSP11303)
  18. 0.379 80E (RSP11212)
  19. 0.375 R1in136 (SRR14708227)
  20. 0.374 Cherry Blossom (RSP11311)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.372 Cbot-2019-005 (RSP11133)
  2. 0.371 USO 31 (RSP10981)
  3. 0.361 Skywalker OG (RSP10837)
  4. 0.352 Monoica (RSP10241)
  5. 0.351 RKM-2018-026 (RSP11118)
  6. 0.351 Kush Hemp E1 (RSP11128)
  7. 0.349 Futura 75 (RSP10664)
  8. 0.338 RKM-2018-002 (RSP11093)
  9. 0.338 Carmagnola (RSP11037)
  10. 0.335 Lovrin (RSP10658)
  11. 0.331 RKM-2018-034 (RSP11126)
  12. 0.330 Fedora 17 (RSP10661)
  13. 0.325 Feral (RSP10890)
  14. 0.322 Blueberry Cheesecake (RSP10672)
  15. 0.318 Carmagnola (RSP10979)
  16. 0.306 JL yellow (RSP11075)
  17. 0.306 Blueberry Cheesecake (RSP10680)
  18. 0.302 Tisza (RSP11044)
  19. 0.301 Jiangji (RSP10653)
  20. 0.295 Kimbo Slice (RSP10997)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR4448263
Overlapping SNPs:
14
Concordance:
13

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495210
Overlapping SNPs:
5
Concordance:
5
QR code for SRR14708261

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