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Detailed information for vg0212840665:

Variant ID: vg0212840665 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 12840665
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACCAAACAACAAAGAACATGCTTGCATAGGGACAAGATCAAAATTGGCAGTATCATGGTAATTCCCAATCGAAAAGTTTATTCTCACAATTCTATTTAC[C/T]
TTGAACTTACCACAAGAGTTGAACCATTTGATGTAATATGGATGAGGATGCGGTTGTGTAAGCAACTCAAGTTTCTCAACCAAATCTGAACTCACAAAGT

Reverse complement sequence

ACTTTGTGAGTTCAGATTTGGTTGAGAAACTTGAGTTGCTTACACAACCGCATCCTCATCCATATTACATCAAATGGTTCAACTCTTGTGGTAAGTTCAA[G/A]
GTAAATAGAATTGTGAGAATAAACTTTTCGATTGGGAATTACCATGATACTGCCAATTTTGATCTTGTCCCTATGCAAGCATGTTCTTTGTTGTTTGGTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.30% 7.80% 7.15% 2.77% NA
All Indica  2759 76.00% 8.80% 10.62% 4.53% NA
All Japonica  1512 99.80% 0.00% 0.20% 0.00% NA
Aus  269 42.40% 43.90% 13.01% 0.74% NA
Indica I  595 88.70% 1.00% 8.40% 1.85% NA
Indica II  465 72.50% 8.60% 15.70% 3.23% NA
Indica III  913 68.70% 14.80% 9.20% 7.34% NA
Indica Intermediate  786 77.10% 7.90% 10.94% 4.07% NA
Temperate Japonica  767 99.70% 0.00% 0.26% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 6.20% 1.04% 0.00% NA
Intermediate  90 86.70% 2.20% 6.67% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0212840665 C -> T LOC_Os02g21620.1 splice_region_variant&synonymous_variant ; p.Lys293Lys; LOW synonymous_codon Average:6.893; most accessible tissue: Zhenshan97 flower, score: 11.396 N N N N
vg0212840665 C -> DEL LOC_Os02g21620.1 N frameshift_variant Average:6.893; most accessible tissue: Zhenshan97 flower, score: 11.396 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0212840665 NA 8.72E-06 mr1048 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 NA 6.02E-06 mr1054 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 NA 8.95E-11 mr1232 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 NA 3.45E-06 mr1287 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 NA 4.92E-06 mr1351 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 NA 4.47E-06 mr1372 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 NA 1.03E-06 mr1382 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 NA 4.61E-06 mr1393 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 1.28E-06 1.27E-06 mr1481 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 NA 3.88E-06 mr1512 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 7.08E-07 7.10E-07 mr1562 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 2.58E-06 2.58E-06 mr1562 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 NA 2.19E-06 mr1646 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 NA 2.18E-06 mr1787 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 3.30E-06 1.59E-06 mr1895 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212840665 4.42E-06 2.05E-06 mr1895 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251