Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0316103102:

Variant ID: vg0316103102 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16103102
Reference Allele: AAlternative Allele: G,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


CCAACATTCTAGAACCAAGCATATTGACATACGCTATCACTTCCTAAAAGACCATGTTGTTGCCAAGAGTGACATAGTCATTAGCCACATAAGAACCGAG[A/G,T]
ATCAACTAGCCGACATATTTACCAAGCCTCTTGATGAAACCCGCTTTTGCAAGTTGAGAAATGAGTTAAATGTCATAGACTTCTCTAATGTGGCTTGAGA

Reverse complement sequence

TCTCAAGCCACATTAGAGAAGTCTATGACATTTAACTCATTTCTCAACTTGCAAAAGCGGGTTTCATCAAGAGGCTTGGTAAATATGTCGGCTAGTTGAT[T/C,A]
CTCGGTTCTTATGTGGCTAATGACTATGTCACTCTTGGCAACAACATGGTCTTTTAGGAAGTGATAGCGTATGTCAATATGCTTGGTTCTAGAATGTTGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.10% 29.80% 0.08% 0.00% T: 0.02%
All Indica  2759 98.70% 1.30% 0.07% 0.00% NA
All Japonica  1512 19.20% 80.80% 0.07% 0.00% NA
Aus  269 80.70% 19.30% 0.00% 0.00% NA
Indica I  595 99.20% 0.50% 0.34% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 52.80% 47.20% 0.00% 0.00% NA
Japonica Intermediate  241 6.60% 92.90% 0.41% 0.00% NA
VI/Aromatic  96 19.80% 79.20% 0.00% 0.00% T: 1.04%
Intermediate  90 72.20% 26.70% 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
vg0316103102 A -> T LOC_Os03g28010.1 missense_variant ; p.Asn1944Tyr; MODERATE nonsynonymous_codon Average:28.995; most accessible tissue: Zhenshan97 panicle, score: 39.652 benign 0.117 DELETERIOUS 0.00
vg0316103102 A -> G LOC_Os03g28010.1 missense_variant ; p.Asn1944Asp; MODERATE nonsynonymous_codon Average:28.995; most accessible tissue: Zhenshan97 panicle, score: 39.652 benign -0.11 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316103102 NA 8.71E-12 mr1940 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
vg0316103102 2.25E-06 NA mr1676_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