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Detailed information for vg0305244603:

Variant ID: vg0305244603 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 5244603
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


GTGTTTCTTGAATCGTGTAAGGCGTTGAAGGCGGCCACTACATCATTTTTGATGATGTCCCAACACGATTTAAAGAACTTCCCTGTAAAACCATTTGGGC[C/T]
TGGTGCCTTGTCGATTGGCATTTCTTTTATTGCTTTGTGGATCTCTACTTCTGTGAAGGGATCGTCTAGCCCGGAGAGATCGATCGGGGTGTATCCGAGA

Reverse complement sequence

TCTCGGATACACCCCGATCGATCTCTCCGGGCTAGACGATCCCTTCACAGAAGTAGAGATCCACAAAGCAATAAAAGAAATGCCAATCGACAAGGCACCA[G/A]
GCCCAAATGGTTTTACAGGGAAGTTCTTTAAATCGTGTTGGGACATCATCAAAAATGATGTAGTGGCCGCCTTCAACGCCTTACACGATTCAAGAAACAC

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 88.40% 11.60% 0.00% 0.00% NA
All Indica  2759 92.20% 7.80% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 1.90% 98.10% 0.00% 0.00% NA
Indica I  595 93.30% 6.70% 0.00% 0.00% NA
Indica II  465 88.80% 11.20% 0.00% 0.00% NA
Indica III  913 97.50% 2.50% 0.00% 0.00% NA
Indica Intermediate  786 87.30% 12.70% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 44.80% 55.20% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0305244603 C -> T LOC_Os03g10280.1 missense_variant ; p.Gly382Ser; MODERATE nonsynonymous_codon ; G382S Average:24.803; most accessible tissue: Minghui63 young leaf, score: 32.638 benign 0.85 DELETERIOUS 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0305244603 NA 1.07E-06 mr1126 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
vg0305244603 NA 9.27E-07 mr1633 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
vg0305244603 NA 6.59E-10 mr1730 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
vg0305244603 NA 7.42E-08 mr1126_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
vg0305244603 NA 6.61E-12 mr1166_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
vg0305244603 NA 6.71E-23 mr1305_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
vg0305244603 3.18E-06 NA mr1458_2 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
vg0305244603 NA 1.09E-08 mr1765_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