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Detailed information for vg0200789612:

Variant ID: vg0200789612 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 789612
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, G: 0.21, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GTATACCGCAATTTCTTTCGATGCTTTTACGCTCAATGCACACAAAACACACGAACTCGATCGATCATATCACACACAATCGTCATCAGAAGAGCAGATC[G/A]
TCACTAGTGGCAGCAAATCCGCCATAGATGTCTCCCATGTTTAGCAGGTCAAAGTAGCCGCCGCCTCCTGCCATTGGAGCAGCAGCAGCTGAGCTCTGAT

Reverse complement sequence

ATCAGAGCTCAGCTGCTGCTGCTCCAATGGCAGGAGGCGGCGGCTACTTTGACCTGCTAAACATGGGAGACATCTATGGCGGATTTGCTGCCACTAGTGA[C/T]
GATCTGCTCTTCTGATGACGATTGTGTGTGATATGATCGATCGAGTTCGTGTGTTTTGTGTGCATTGAGCGTAAAAGCATCGAAAGAAATTGCGGTATAC

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 73.60% 26.30% 0.08% 0.00% NA
All Indica  2759 90.40% 9.50% 0.11% 0.00% NA
All Japonica  1512 60.40% 39.60% 0.00% 0.00% NA
Aus  269 8.60% 91.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 73.50% 26.00% 0.43% 0.00% NA
Indica III  913 95.60% 4.40% 0.00% 0.00% NA
Indica Intermediate  786 87.00% 12.80% 0.13% 0.00% NA
Temperate Japonica  767 83.30% 16.70% 0.00% 0.00% NA
Tropical Japonica  504 18.80% 81.20% 0.00% 0.00% NA
Japonica Intermediate  241 74.30% 25.70% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 51.10% 47.80% 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
vg0200789612 G -> A LOC_Os02g02370.1 synonymous_variant ; p.Asp293Asp; LOW synonymous_codon Average:73.392; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200789612 NA 2.12E-06 mr1092 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
vg0200789612 NA 7.26E-07 mr1154 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
vg0200789612 NA 9.29E-06 mr1740 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
vg0200789612 NA 7.89E-06 mr1559_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
vg0200789612 NA 1.06E-07 mr1642_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
vg0200789612 NA 9.86E-07 mr1762_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