Mexican Sativa
SRR 14708263
General Information
- Sample Name
- MSA
- Accession Date
- May 31, 2021
- Reported Plant Sex
- not reported
- Report Type
- Whole-Genome Sequencing
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.
Chemical Information
Cannabinoid and terpenoid information provided by the grower.
Cannabinoids
No information provided.
Terpenoids
No information provided.
Genetic Information
- Plant Type
- Type II
File Downloads
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.
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.

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).



This chart represents the Illumina sequence coverage over the CBCA synthase gene.

Variants (THCAS, CBDAS, and CBCAS)
No variants to report
Variants (Select Genes of Interest)
GPPs1 |
c.845_848del |
p.Glu282fs | frameshift variant | high | contig676 | 169629 | TGAAA/T |
|
PHL-2 | c.44G>A | p.Arg15Lys | missense variant | moderate | contig2621 | 337613 | G/A | |
PKSG-4b |
c.353_354ins |
p.Gly119fs | frameshift variant | high | contig700 | 2721319 | T/TGG |
|
PKSG-4b | c.229G>A | p.Gly77Ser | missense variant | moderate | contig700 | 2724206 | C/T |
|
PKSG-4b | c.216G>C | p.Leu72Phe | missense variant | moderate | contig700 | 2724219 | C/G |
|
PKSG-4b | c.206T>C | p.Leu69Ser | missense variant | moderate | contig700 | 2724229 | A/G |
|
PKSG-2a | c.67T>A | p.Phe23Ile | missense variant | moderate | contig700 | 1945567 | A/T | |
PKSG-2a | c.31A>T | p.Thr11Ser | missense variant | moderate | contig700 | 1945603 | T/A | |
DXR-2 | c.1319T>C | p.Ile440Thr | missense variant | moderate | contig380 | 285250 | A/G |
|
ELF3 | c.520A>C | p.Asn174His | missense variant | moderate | contig97 | 242226 | A/C | |
aPT1 | c.670T>A | p.Ser224Thr | missense variant | moderate | contig121 | 2840278 | T/A |
|
AAE1-2 | c.1415G>A | p.Ser472Asn | missense variant | moderate | contig81 | 210377 | G/A |
|
AAE1-2 | c.1417A>G | p.Thr473Ala | missense variant | moderate | contig81 | 210379 | A/G |
|
AAE1-2 | c.1434G>T | p.Glu478Asp | missense variant | moderate | contig81 | 210396 | G/T |
|
PHL-1 |
c.3488_3499d |
p.Ala1163_Il |
disruptive inframe deletion | moderate | contig1439 | 1485421 |
ATTCCAACACTA |
|
PHL-1 | c.2551A>G | p.Thr851Ala | missense variant | moderate | contig1439 | 1487246 | T/C | |
PHL-1 | c.176G>A | p.Gly59Glu | missense variant | moderate | contig1439 | 1492817 | C/T |
|
PHL-1 | c.175G>A | p.Gly59Arg | missense variant | moderate | contig1439 | 1492818 | C/T | |
Edestin | c.16T>C | p.Ser6Pro | missense variant | moderate | contig850 | 3065274 | A/G |
|
PKSG-2b | c.1152T>A | p.Asn384Lys | missense variant | moderate | contig700 | 1950486 | A/T | |
PKSG-2b | c.1132C>G | p.Leu378Val | missense variant | moderate | contig700 | 1950506 | G/C |
|
PKSG-2b | c.1117A>G | p.Ile373Val | missense variant | moderate | contig700 | 1950521 | T/C | |
PKSG-2b | c.-2_1dupATA | start lost & conservative inframe insertion | high | contig700 | 1951880 | A/ATAT |
|
|
TFL1 | c.47_48dupAT | p.Val17fs | frameshift variant | high | contig1636 | 521258 | C/CAT | |
HDS-1 | c.2141G>C | p.Gly714Ala | missense variant | moderate | contig1891 | 884225 | C/G |
|
HDS-1 | c.1475C>A | p.Pro492Gln | missense variant | moderate | contig1891 | 886162 | G/T |
|
HDS-1 | c.1393G>A | p.Ala465Thr | missense variant & splice region variant | moderate | contig1891 | 886355 | C/T | |
HDS-1 | c.1378G>A | p.Val460Ile | missense variant | moderate | contig1891 | 886370 | C/T |
|
HDS-1 |
c.-108+1_-10 |
splice donor variant & intron variant | high | contig1891 | 889975 | A/AC |
|
|
PIE1-2 | c.1630G>C | p.Ala544Pro | missense variant | moderate | contig1460 | 1191600 | C/G | |
EMF2 |
c.1415_1416i |
p.His474fs | frameshift variant | high | contig954 | 3056602 | A/ATT |
|
EMF2 |
c.1418_1419i |
p.Ser473_His |
disruptive inframe insertion | moderate | contig954 | 3056605 | C/CACA | |
EMF2 |
c.1419_1420i |
p.His474fs | frameshift variant | high | contig954 | 3056606 | G/GT |
|
aPT4 | c.80A>G | p.Lys27Arg | missense variant | moderate | contig121 | 2828736 | A/G |
|
aPT4 | c.202T>A | p.Leu68Ile | missense variant | moderate | contig121 | 2828858 | T/A |
|
AAE1-3 | c.722G>A | p.Arg241Lys | missense variant | moderate | contig976 | 1083132 | C/T |
|
AAE1-3 | c.659G>A | p.Arg220Gln | missense variant | moderate | contig976 | 1083195 | C/T |
|
AAE1-3 | c.475G>A | p.Gly159Arg | missense variant | moderate | contig976 | 1083550 | C/T |
|
AAE1-3 | c.52G>A | p.Gly18Ser | missense variant | moderate | contig976 | 1084023 | C/T |
|
PKSB-3 |
c.1880_1891d |
p.His627_Gly |
disruptive inframe deletion | moderate | contig93 | 3339981 |
CTGGCCATGGCC |
|
Nearest genetic relatives (All Samples)
- 0.140 B52 (SRR14708255)
- 0.141 AOAC MI 533 (RSP11753)
- 0.144 AOAC MI 504 (RSP11749)
- 0.147 Electra (RSP11366)
- 0.149 AOAC MI 535 (RSP11754)
- 0.150 AOAC MI 567 (RSP11758)
- 0.151 AOAC MI 597 (RSP11761)
- 0.152 AOAC MI 501 (RSP11748)
- 0.152 AOAC MI 532 (RSP11752)
- 0.153 AOAC MI 588 (RSP11760)
- 0.154 AOAC MI 545 (RSP11756)
- 0.156 AOAC MI 542 (RSP11755)
- 0.157 AOAC MI 508 (RSP11750)
- 0.158 AOAC MI 599 (RSP11762)
- 0.160 AOAC MI 548 (RSP11757)
- 0.161 Lift (RSP11378)
- 0.167 AOAC MI 569 (RSP11759)
- 0.177 Blue Dream (RSP11006)
- 0.178 Doug s Varin (RSP11243)
- 0.178 Blue Dream (RSP11004)
Nearest genetic relatives (Base Tree)
- 0.192 Liberty Haze (RSP11000)
- 0.221 UP Sunrise (RSP10989)
- 0.225 KYRG-11 (RSP11051)
- 0.228 Golden Goat 2 (RSP10991)
- 0.230 Cherry (RSP11143)
- 0.240 Blueberry Cheesecake (RSP10684)
- 0.244 RKM-2018-020 (RSP11112)
- 0.246 QUEEN JESUS (RSP10105)
- 0.247 Tisza (RSP10659)
- 0.248 Blue Dream (RSP11033)
- 0.248 RKM-2018-019 (RSP11111)
- 0.250 Tygra (RSP10667)
- 0.259 Tisza (RSP11044)
- 0.260 Recon (RSP10755)
- 0.264 Gold Cracker (RSP11048)
- 0.266 RKM-2018-028 (RSP11120)
- 0.266 RKM-2018-031 (RSP11123)
- 0.266 RKM-2018-003 (RSP11094)
- 0.268 Hermaphrodite Research Sample1 (RSP11049)
- 0.270 Italian Kiss (RSP11034)
Most genetically distant strains (All Samples)
- 0.420 JL 3rd Gen Mother (RSP11214)
- 0.398 JL yellow (RSP11075)
- 0.389 JL 4th Gen 5 (RSP11199)
- 0.378 JL 3rd Gen Mother (RSP11197)
- 0.378 JL 3rd Gen Father (RSP11196)
- 0.378 JL 4th Gen 1 (RSP11193)
- 0.376 80E (RSP11213)
- 0.371 Tanao Sri-white 80 (RSP11621)
- 0.370 Cherry Blossom (RSP11323)
- 0.369 Kush Hemp E1 (RSP11128)
- 0.366 Feral (RSP11205)
- 0.365 Tiborszallasie (RSP11210)
- 0.364 Ivory (RSP10668)
- 0.364 CS (RSP11208)
- 0.363 Cherry Blossom (RSP11318)
- 0.361 JL 4th Gen 4 (RSP11198)
- 0.361 Red Eye OG (RSP11190)
- 0.355 Unknown- Cherry Wine - 001 (RSP11268)
- 0.355 Feral (RSP11206)
- 0.354 Wife (RSP11148)
Most genetically distant strains (Base Tree)
- 0.381 JL yellow (RSP11075)
- 0.353 Kush Hemp E1 (RSP11128)
- 0.351 Cbot-2019-005 (RSP11133)
- 0.346 Fedora 17 (RSP10661)
- 0.345 Ivory (RSP10668)
- 0.341 Skywalker OG (RSP10837)
- 0.341 Blueberry Cheesecake (RSP10680)
- 0.340 Monoica (RSP10241)
- 0.337 RKM-2018-033 (RSP11125)
- 0.333 RKM-2018-034 (RSP11126)
- 0.328 RKM-2018-026 (RSP11118)
- 0.328 Carmagnola (RSP10979)
- 0.328 Black Beauty (RSP11035)
- 0.328 RKM-2018-006 (RSP11097)
- 0.327 Cbot-2019-004 (RSP11132)
- 0.326 Sour Raspberry (RSP10551)
- 0.326 RKM-2018-002 (RSP11093)
- 0.313 Kimbo Slice (RSP10997)
- 0.308 Skunk 18 (RSP11038)
- 0.307 Santhica27 (RSP11047)
Nearest genetic relative in Phylos dataset
- Overlapping SNPs:
- 12
- Concordance:
- 11
Nearest genetic relative in Lynch dataset
- Overlapping SNPs:
- 4
- Concordance:
- 4