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Detailed information for vg0316108526:

Variant ID: vg0316108526 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16108526
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, T: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


AATCCTACAAGAGGGCCTGACCAGCCGAAGCGTCACGTGGTTCTCCCAGGCAAAAGAAAAATCGTAGGAGGTGAGGACAAGACTGACGAGGATTACGATC[A/T]
GTTGGATGGGCAACCCCCTTTCACGGTGACGATTGAGCCTAGCATCCTCCTATCAAATGAAGACACCCCTTACTCACGTAGCGATCACAAGGAGGGAACA

Reverse complement sequence

TGTTCCCTCCTTGTGATCGCTACGTGAGTAAGGGGTGTCTTCATTTGATAGGAGGATGCTAGGCTCAATCGTCACCGTGAAAGGGGGTTGCCCATCCAAC[T/A]
GATCGTAATCCTCGTCAGTCTTGTCCTCACCTCCTACGATTTTTCTTTTGCCTGGGAGAACCACGTGACGCTTCGGCTGGTCAGGCCCTCTTGTAGGATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.70% 49.10% 0.19% 0.00% NA
All Indica  2759 19.10% 80.60% 0.29% 0.00% NA
All Japonica  1512 97.00% 3.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 15.00% 84.90% 0.17% 0.00% NA
Indica II  465 9.20% 90.10% 0.65% 0.00% NA
Indica III  913 25.80% 73.90% 0.22% 0.00% NA
Indica Intermediate  786 20.20% 79.50% 0.25% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 92.50% 7.50% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 55.60% 43.30% 1.11% 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
vg0316108526 A -> T LOC_Os03g28020.1 missense_variant ; p.Gln489Leu; MODERATE nonsynonymous_codon ; Q489L Average:38.745; most accessible tissue: Zhenshan97 panicle, score: 52.263 benign 0.297 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316108526 NA 6.48E-15 mr1156 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
vg0316108526 NA 4.79E-19 mr1179 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
vg0316108526 NA 4.16E-13 mr1581 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
vg0316108526 NA 2.83E-09 mr1663 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
vg0316108526 NA 3.37E-11 mr1713 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
vg0316108526 NA 1.92E-07 mr1717 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
vg0316108526 NA 1.96E-10 mr1720 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
vg0316108526 NA 5.24E-49 mr1798 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
vg0316108526 NA 2.61E-15 mr1720_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