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Detailed information for vg0129861515:

Variant ID: vg0129861515 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29861515
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TCACTTTATATAAAATTGAAAACACATGAGATGAATGTTCTTTCTCGAAAAGTTGATTCTAAGTCGAGTGCTTTGGTTTCTTCTTCTTCCTCTTTGGATG[C/T]
TGATGCTTCTTCATCTAAGTCTTCTTTTCTTGCTGTTTTTAATGCCACATCCGATGATCAACTCGAACAAATCGAGGAGGAGGATTTGGCTTTGGTTGCT

Reverse complement sequence

AGCAACCAAAGCCAAATCCTCCTCCTCGATTTGTTCGAGTTGATCATCGGATGTGGCATTAAAAACAGCAAGAAAAGAAGACTTAGATGAAGAAGCATCA[G/A]
CATCCAAAGAGGAAGAAGAAGAAACCAAAGCACTCGACTTAGAATCAACTTTTCGAGAAAGAACATTCATCTCATGTGTTTTCAATTTTATATAAAGTGA

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 27.40% 10.30% 28.29% 34.00% NA
All Indica  2759 6.50% 5.50% 34.87% 53.17% NA
All Japonica  1512 71.40% 1.30% 20.17% 7.21% NA
Aus  269 0.40% 83.60% 10.04% 5.95% NA
Indica I  595 4.20% 1.70% 50.25% 43.87% NA
Indica II  465 10.50% 0.90% 35.05% 53.55% NA
Indica III  913 3.50% 7.20% 26.51% 62.76% NA
Indica Intermediate  786 9.20% 9.20% 32.82% 48.85% NA
Temperate Japonica  767 99.10% 0.10% 0.39% 0.39% NA
Tropical Japonica  504 21.80% 1.40% 56.94% 19.84% NA
Japonica Intermediate  241 86.70% 4.60% 6.22% 2.49% NA
VI/Aromatic  96 3.10% 78.10% 15.62% 3.12% NA
Intermediate  90 36.70% 18.90% 31.11% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0129861515 C -> T LOC_Os01g51950.1 missense_variant ; p.Ala183Val; MODERATE nonsynonymous_codon ; A183V Average:14.312; most accessible tissue: Minghui63 young leaf, score: 20.156 benign -0.674 TOLERATED 1.00
vg0129861515 C -> DEL LOC_Os01g51950.1 N frameshift_variant Average:14.312; most accessible tissue: Minghui63 young leaf, score: 20.156 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129861515 NA 2.17E-13 mr1010 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
vg0129861515 6.46E-06 NA mr1083 Ind_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
vg0129861515 NA 5.26E-10 mr1277 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
vg0129861515 NA 4.21E-07 mr1584 Jap_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
vg0129861515 1.10E-06 5.72E-07 mr1720 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
vg0129861515 NA 2.01E-14 mr1740 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
vg0129861515 NA 4.03E-09 mr1746 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
vg0129861515 NA 1.02E-06 mr1748 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
vg0129861515 NA 4.67E-06 mr1837 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
vg0129861515 NA 6.94E-15 mr1982 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
vg0129861515 NA 1.04E-06 mr1097_2 Jap_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
vg0129861515 NA 1.60E-11 mr1520_2 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
vg0129861515 NA 8.10E-15 mr1539_2 Jap_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