Advanced Strain Search

PCL2

SRR 14708245

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: 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 III

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.

Heterozygosity: 1.21%
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: 0.0206
male female SRR14708245

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.1420A>C p.Lys474Gln missense variant moderate contig1772 2083646

IGV: Start, Jump

A/C
NGS:
0.132
C90:
0.813
CBDAS c.1628G>A p.Arg543His missense variant moderate contig1772 2083854

IGV: Start, Jump

G/A
NGS:
0.033
C90:
0.000

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.1837G>A p.Glu613Lys missense variant moderate contig2621 341115

IGV: Start, Jump

G/A
NGS:
0.009
C90:
0.000
PHL-2 c.2564T>A p.Phe855Tyr missense variant moderate contig2621 342607

IGV: Start, Jump

T/A
NGS:
0.064
C90:
0.732
PKSG-2a

UniProt

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

IGV: Start, Jump

A/T
NGS:
0.825
C90:
0.904
DXR-2

UniProt

c.1319T>C p.Ile440Thr missense variant moderate contig380 285250

IGV: Start, Jump

A/G
NGS:
0.480
C90:
0.000
ELF4

UniProt

c.144T>A p.Asp48Glu missense variant moderate contig869 622426

IGV: Start, Jump

A/T
NGS:
0.031
C90:
0.000
ELF3

UniProt

c.574A>G p.Asn192Asp missense variant moderate contig97 242280

IGV: Start, Jump

A/G
NGS:
0.042
C90:
0.579
OAC-1

UniProt

c.260C>G p.Ser87Cys missense variant moderate contig931 118104

IGV: Start, Jump

G/C
NGS:
0.053
C90:
0.000
OAC-1

UniProt

c.52G>T p.Ala18Ser missense variant moderate contig931 118412

IGV: Start, Jump

C/A
NGS:
0.000
C90:
0.000
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
PKSG-2b

UniProt

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

IGV: Start, Jump

A/T
NGS:
0.715
C90:
0.895
TFL1

UniProt

c.368G>T p.Arg123Met missense variant moderate contig1636 520549

IGV: Start, Jump

C/A
NGS:
0.000
C90:
0.000
TFL1

UniProt

c.358G>A p.Gly120Arg missense variant moderate contig1636 520559

IGV: Start, Jump

C/T
NGS:
0.000
C90:
0.000
TFL1

UniProt

c.304G>A p.Asp102Asn missense variant & splice region variant moderate contig1636 520613

IGV: Start, Jump

C/T
NGS:
0.024
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.-108+1_-108+2insG splice donor variant & intron variant high contig1891 889975

IGV: Start, Jump

A/AC
NGS:
0.217
C90:
0.000
EMF1-1

UniProt

c.627_629dupTGT p.Val210dup disruptive inframe insertion moderate contig883 270231

IGV: Start, Jump

A/ATGT
NGS:
0.007
C90:
0.000
FT

UniProt

c.240C>G p.Asn80Lys missense variant moderate contig1561 3124664

IGV: Start, Jump

C/G
NGS:
0.075
C90:
0.000
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.97T>C p.Tyr33His missense variant moderate contig121 2828753

IGV: Start, Jump

T/C
NGS:
0.439
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
FLD

UniProt

c.2810+2T>C splice donor variant & intron variant high contig1450 2044250

IGV: Start, Jump

A/G
NGS:
0.000
C90:
0.000
FLD

UniProt

c.2746A>G p.Asn916Asp missense variant moderate contig1450 2044531

IGV: Start, Jump

T/C
NGS:
0.004
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.260T>C p.Val87Ala missense variant moderate contig976 1083765

IGV: Start, Jump

A/G
NGS:
0.000
C90:
0.000

Nearest genetic relatives (All Samples)

0 0.075 0.150 0.225 0.300
clone distance sibling distance more distant
  1. 0.166 PCL1 (SRR14708246)
  2. 0.251 PID2 (SRR14708247)
  3. 0.262 KYRG-151 (RSP11052)
  4. 0.264 IBR1 (SRR14708251)
  5. 0.265 IUL1 (SRR14708254)
  6. 0.266 YNN (SRR14708199)
  7. 0.267 IMA (SRR14708203)
  8. 0.268 IBR3 (SRR14708249)
  9. 0.268 IBR2 (SRR14708250)
  10. 0.268 Jiangji (RSP10653)
  11. 0.269 PID1 (SRR14708248)
  12. 0.270 Kyrgyz Gold (RSP11054)
  13. 0.270 Carmagnola (RSP10982)
  14. 0.271 R3 (RSP11616)
  15. 0.271 Tak-HN (RSP11618)
  16. 0.272 IBE (SRR14708228)
  17. 0.273 Tiger Tail -78- (RSP11619)
  18. 0.273 R2 (RSP11615)
  19. 0.274 IUL2 (SRR14708253)
  20. 0.274 IUP1 (SRR14708258)

Nearest genetic relatives (Base Tree)

0 0.083 0.167 0.250 0.333
clone distance sibling distance more distant
  1. 0.265 Kyrgyz Gold (RSP11054)
  2. 0.273 Jiangji (RSP10653)
  3. 0.273 KYRG-11 (RSP11051)
  4. 0.285 Tisza (RSP10659)
  5. 0.291 Lovrin (RSP10658)
  6. 0.293 Futura 75 (RSP10664)
  7. 0.295 Tisza (RSP11044)
  8. 0.296 Carmagnola (RSP11037)
  9. 0.302 Tygra (RSP10667)
  10. 0.303 Fedora 17 (RSP10661)
  11. 0.304 Ivory (RSP10668)
  12. 0.306 Carmagnola (RSP10979)
  13. 0.308 Monoica (RSP10241)
  14. 0.312 Santhica27 (RSP11047)
  15. 0.316 Feral (RSP10890)
  16. 0.318 RKM-2018-029 (RSP11121)
  17. 0.318 Recon (RSP10755)
  18. 0.322 Hermaphrodite ResearchSample2 (RSP11050)
  19. 0.326 USO 31 (RSP10981)
  20. 0.330 Kimbo Slice (RSP10997)

Most genetically distant strains (All Samples)

0 0.117 0.233 0.350 0.467
clone distance sibling distance more distant
  1. 0.465 Cherry Blossom (RSP11318)
  2. 0.449 Cherry Blossom (RSP11301)
  3. 0.440 Cherry Blossom (RSP11323)
  4. 0.438 Cherry Blossom (RSP11300)
  5. 0.433 Unknown--Cherry Wine---001- (RSP11268)
  6. 0.431 Cherry Blossom (RSP11331)
  7. 0.429 Chem 91 (RSP11185)
  8. 0.429 Cherry Blossom (RSP11311)
  9. 0.429 CHEM4 (RSP12090)
  10. 0.427 Queen Dream (RSP11278)
  11. 0.426 Queen Dream CBG (RSP11287)
  12. 0.426 GG4 (RSP11978)
  13. 0.424 QLE1 (RSP11451)
  14. 0.424 Cherry Blossom (RSP11328)
  15. 0.421 Cherry Blossom (RSP11302)
  16. 0.421 Cherry Blossom (RSP11312)
  17. 0.421 New York City Deisel (RSP11225)
  18. 0.421 JL x NSPM1 4 (RSP11482)
  19. 0.420 Cherry Blossom (RSP11333)
  20. 0.419 Cherry Blossom (RSP11334)

Most genetically distant strains (Base Tree)

0 0.108 0.217 0.325 0.433
clone distance sibling distance more distant
  1. 0.418 RKM-2018-002 (RSP11093)
  2. 0.403 RKM-2018-028 (RSP11120)
  3. 0.399 JL yellow (RSP11075)
  4. 0.397 Skywalker OG (RSP10837)
  5. 0.395 Cbot-2019-005 (RSP11133)
  6. 0.395 RKM-2018-032 (RSP11124)
  7. 0.395 RKM-2018-022 (RSP11114)
  8. 0.393 Kush Hemp E1 (RSP11128)
  9. 0.391 RKM-2018-018 (RSP11110)
  10. 0.389 RKM-2018-023 (RSP11115)
  11. 0.387 Cherry (RSP11142)
  12. 0.386 Skunk#18 (RSP11038)
  13. 0.385 RKM-2018-004 (RSP11096)
  14. 0.384 RKM-2018-026 (RSP11118)
  15. 0.383 Hermaphrodite Research Sample1 (RSP11049)
  16. 0.379 Blue Dream (RSP11033)
  17. 0.378 Italian Kiss (RSP11034)
  18. 0.377 Golden Goat 2 (RSP10991)
  19. 0.377 RKM-2018-033 (RSP11125)
  20. 0.375 Cbot-2019-001 (RSP11129)

Nearest genetic relative in Phylos dataset

Phylos Strain SRR8346566
Overlapping SNPs:
14
Concordance:
12

Nearest genetic relative in Lynch dataset

Lynch Strain SRR3495181
Overlapping SNPs:
3
Concordance:
3
QR code for SRR14708245

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