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Detailed information for vg0130094621:

Variant ID: vg0130094621 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 30094621
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.08, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TAATGTTTTAGCTATTAGCATGGAGTCTCCCACTTTTCGAATTTGCGCTACTATTGTACATTGCGGCCGTGTTTAGATCTAAAGTTTTTCTTCAAACTTC[C/T]
AACTTTTCCATCACATCAAAACTTTCCTACACACAAACTTTTAACTTTTCCGTCACATCGTTCCAATTTTAATCAAACTTCTAATTTTGGCGGGAACTAA

Reverse complement sequence

TTAGTTCCCGCCAAAATTAGAAGTTTGATTAAAATTGGAACGATGTGACGGAAAAGTTAAAAGTTTGTGTGTAGGAAAGTTTTGATGTGATGGAAAAGTT[G/A]
GAAGTTTGAAGAAAAACTTTAGATCTAAACACGGCCGCAATGTACAATAGTAGCGCAAATTCGAAAAGTGGGAGACTCCATGCTAATAGCTAAAACATTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.10% 36.80% 0.11% 0.00% NA
All Indica  2759 96.40% 3.50% 0.14% 0.00% NA
All Japonica  1512 0.80% 99.20% 0.00% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 95.10% 4.50% 0.34% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 97.90% 2.10% 0.00% 0.00% NA
Indica Intermediate  786 94.10% 5.60% 0.25% 0.00% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 20.80% 79.20% 0.00% 0.00% NA
Intermediate  90 33.30% 65.60% 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
vg0130094621 C -> T LOC_Os01g52380.1 downstream_gene_variant ; 1435.0bp to feature; MODIFIER silent_mutation Average:47.127; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0130094621 C -> T LOC_Os01g52390.1 downstream_gene_variant ; 799.0bp to feature; MODIFIER silent_mutation Average:47.127; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0130094621 C -> T LOC_Os01g52380-LOC_Os01g52390 intergenic_region ; MODIFIER silent_mutation Average:47.127; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0130094621 NA 6.38E-06 mr1152 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
vg0130094621 4.80E-06 NA mr1252 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
vg0130094621 1.11E-06 1.15E-06 mr1252 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
vg0130094621 NA 7.24E-35 mr1542 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