Mexican Sativa

SRR 14708263

Grower: Lanzhou University, Guangpeng Ren

General Information

Sample Name
MSA
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
Type II

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: 0.0612
male female SRR14708263

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
PHL-2 c.44G>A p.Arg15Lys missense variant moderate contig2621 337613

IGV: Start, Jump

G/A
NGS:
0.015
C90:
0.167
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.229G>A p.Gly77Ser missense variant moderate contig700 2724206

IGV: Start, Jump

C/T
NGS:
0.042
C90:
0.000
PKSG-4b

UniProt

c.216G>C p.Leu72Phe missense variant moderate contig700 2724219

IGV: Start, Jump

C/G
NGS:
0.044
C90:
0.000
PKSG-4b

UniProt

c.206T>C p.Leu69Ser missense variant moderate contig700 2724229

IGV: Start, Jump

A/G
NGS:
0.044
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
PKSG-2a

UniProt

c.31A>T p.Thr11Ser missense variant moderate contig700 1945603

IGV: Start, Jump

T/A
NGS:
0.763
C90:
0.876
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
aPT1

UniProt

c.670T>A p.Ser224Thr missense variant moderate contig121 2840278

IGV: Start, Jump

T/A
NGS:
0.077
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.3488_3499delCTAGTGTTGGAA p.Ala1163_Ile1167delinsVal disruptive inframe deletion moderate contig1439 1485421

IGV: Start, Jump

ATTCCAACACTAG/A
NGS:
0.000
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.176G>A p.Gly59Glu missense variant moderate contig1439 1492817

IGV: Start, Jump

C/T
NGS:
0.024
C90:
0.000
PHL-1

UniProt

c.175G>A p.Gly59Arg missense variant moderate contig1439 1492818

IGV: Start, Jump

C/T
NGS:
0.024
C90:
0.144
Edestin

UniProt

c.16T>C p.Ser6Pro missense variant moderate contig850 3065274

IGV: Start, Jump

A/G
NGS:
0.059
C90:
0.000
PKSG-2b

UniProt

c.1152T>A p.Asn384Lys missense variant moderate contig700 1950486

IGV: Start, Jump

A/T
NGS:
0.715
C90:
0.895
PKSG-2b

UniProt

c.1132C>G p.Leu378Val missense variant moderate contig700 1950506

IGV: Start, Jump

G/C
NGS:
0.717
C90:
0.000
PKSG-2b

UniProt

c.1117A>G p.Ile373Val missense variant moderate contig700 1950521

IGV: Start, Jump

T/C
NGS:
0.807
C90:
0.981
PKSG-2b

UniProt

c.-2_1dupATA start lost & conservative inframe insertion high contig700 1951880

IGV: Start, Jump

A/ATAT
NGS:
0.410
C90:
0.000
TFL1

UniProt

c.47_48dupAT p.Val17fs frameshift variant high contig1636 521258

IGV: Start, Jump

C/CAT
NGS:
0.026
C90:
0.211
HDS-1

UniProt

c.2141G>C p.Gly714Ala missense variant moderate contig1891 884225

IGV: Start, Jump

C/G
NGS:
0.018
C90:
0.000
HDS-1

UniProt

c.1475C>A p.Pro492Gln missense variant moderate contig1891 886162

IGV: Start, Jump

G/T
NGS:
0.011
C90:
0.000
HDS-1

UniProt

c.1393G>A p.Ala465Thr missense variant & splice region variant moderate contig1891 886355

IGV: Start, Jump

C/T
NGS:
0.009
C90:
0.091
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
PIE1-2

UniProt

c.1630G>C p.Ala544Pro missense variant moderate contig1460 1191600

IGV: Start, Jump

C/G
NGS:
0.070
C90:
0.933
EMF2

UniProt

c.1415_1416insTT p.His474fs frameshift variant high contig954 3056602

IGV: Start, Jump

A/ATT
NGS:
0.007
C90:
0.000
EMF2

UniProt

c.1418_1419insACA p.Ser473_His474insGln disruptive inframe insertion moderate contig954 3056605

IGV: Start, Jump

C/CACA
NGS:
0.007
C90:
0.029
EMF2

UniProt

c.1419_1420insT p.His474fs frameshift variant high contig954 3056606

IGV: Start, Jump

G/GT
NGS:
0.004
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.202T>A p.Leu68Ile missense variant moderate contig121 2828858

IGV: Start, Jump

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

UniProt

c.722G>A p.Arg241Lys missense variant moderate contig976 1083132

IGV: Start, Jump

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

UniProt

c.659G>A p.Arg220Gln missense variant moderate contig976 1083195

IGV: Start, Jump

C/T
NGS:
0.077
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.52G>A p.Gly18Ser missense variant moderate contig976 1084023

IGV: Start, Jump

C/T
NGS:
0.064
C90:
0.000
PKSB-3

UniProt

c.1880_1891delATGGCCATGGCC p.His627_Gly630del disruptive inframe deletion moderate contig93 3339981

IGV: Start, Jump

CTGGCCATGGCCA/C
NGS:
0.004
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.075 0.150 0.225 0.300
clone distance sibling distance more distant
  1. 0.271 Blueberry Cheesecake (RSP10684)
  2. 0.272 Liberty Haze (RSP11000)
  3. 0.277 SCN (SRR14708201)
  4. 0.278 Electra (RSP11366)
  5. 0.279 RKM-2018-008 (RSP11099)
  6. 0.280 Tak-HN (RSP11618)
  7. 0.280 Serious Happiness (RSP10763)
  8. 0.281 Pure Power Plant (RSP11265)
  9. 0.283 Domnesia (RSP11184)
  10. 0.286 Kimbo Slice (RSP10997)
  11. 0.286 G13 (RSP11460)
  12. 0.286 The Gift (RSP10988)
  13. 0.287 Liberty Haze (RSP10946)
  14. 0.287 Rest (RSP11377)
  15. 0.288 Tisza (RSP10659)
  16. 0.288 Durban Poison #1 (RSP11013)
  17. 0.289 Doug s Varin (RSP11243)
  18. 0.289 LEMONCAKE (RSP11340)
  19. 0.290 IUL2 (SRR14708253)
  20. 0.291 Cbot-2019-006 (RSP11134)

Nearest genetic relatives (Base Tree)

0 0.083 0.167 0.250 0.333
clone distance sibling distance more distant
  1. 0.273 The Gift (RSP10988)
  2. 0.275 Tisza (RSP11044)
  3. 0.280 Blueberry Cheesecake (RSP10684)
  4. 0.281 Tisza (RSP10659)
  5. 0.290 Kimbo Slice (RSP10997)
  6. 0.292 Recon (RSP10755)
  7. 0.293 Tygra (RSP10667)
  8. 0.295 Jiangji (RSP10653)
  9. 0.296 Liberty Haze (RSP11000)
  10. 0.296 Ivory (RSP10668)
  11. 0.296 Golden Goat 2 (RSP10991)
  12. 0.297 Cbot-2019-006 (RSP11134)
  13. 0.298 Lovrin (RSP10658)
  14. 0.298 CST (RSP11002)
  15. 0.298 Futura 75 (RSP10664)
  16. 0.299 Pie Hoe (RSP11073)
  17. 0.303 Kyrgyz Gold (RSP11054)
  18. 0.304 Carmagnola (RSP11037)
  19. 0.306 Santhica27 (RSP11047)
  20. 0.306 Gold Cracker (RSP11048)

Most genetically distant strains (All Samples)

0 0.125 0.250 0.375 0.500
clone distance sibling distance more distant
  1. 0.467 Cherry Blossom (RSP11318)
  2. 0.459 Cherry Blossom (RSP11328)
  3. 0.458 Cherry Blossom (RSP11323)
  4. 0.444 Unknown--Cherry Wine---001- (RSP11268)
  5. 0.443 Cherry Blossom (RSP11301)
  6. 0.421 Cherry Blossom (RSP11309)
  7. 0.419 Cherry Blossom (RSP11334)
  8. 0.417 Cherry Blossom (RSP11300)
  9. 0.415 Cherry Blossom (RSP11321)
  10. 0.410 Cherry Blossom (RSP11322)
  11. 0.409 Cherry Blossom (RSP11311)
  12. 0.408 Cherry Blossom (RSP11274)
  13. 0.408 Cherry Blossom (RSP11302)
  14. 0.403 Cherry Blossom (RSP11333)
  15. 0.403 Cherry Blossom (RSP11313)
  16. 0.403 Cherry Blossom (RSP11314)
  17. 0.403 Cherry Blossom (RSP11310)
  18. 0.402 Cherry Blossom (RSP11298)
  19. 0.401 Northern Skunk (RSP11456)
  20. 0.401 Unknown--Cherry Wine---002- (RSP11269)

Most genetically distant strains (Base Tree)

0 0.100 0.200 0.300 0.400
clone distance sibling distance more distant
  1. 0.382 JL yellow (RSP11075)
  2. 0.367 Cbot-2019-005 (RSP11133)
  3. 0.364 RKM-2018-006 (RSP11097)
  4. 0.361 RKM-2018-026 (RSP11118)
  5. 0.358 Skunk#18 (RSP11038)
  6. 0.356 Cherry (RSP11142)
  7. 0.353 RKM-2018-028 (RSP11120)
  8. 0.352 RKM-2018-004 (RSP11096)
  9. 0.345 Cbot-2019-001 (RSP11129)
  10. 0.345 RKM-2018-009 (RSP11100)
  11. 0.345 RKM-2018-002 (RSP11093)
  12. 0.343 RKM-2018-022 (RSP11114)
  13. 0.340 RKM-2018-033 (RSP11125)
  14. 0.339 RKM-2018-027 (RSP11119)
  15. 0.338 Black Beauty (RSP11035)
  16. 0.337 RKM-2018-003 (RSP11094)
  17. 0.336 Sour Raspberry (RSP10551)
  18. 0.333 UP Sunrise (RSP10989)
  19. 0.333 Skywalker OG (RSP10837)
  20. 0.333 Feral (RSP10890)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR8349252
Overlapping SNPs:
12
Concordance:
11

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495169
Overlapping SNPs:
4
Concordance:
4
QR code for SRR14708263

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