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Detailed information for vg0903407270:

Variant ID: vg0903407270 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 3407270
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TCCCTAACTTGCTTCATTAGCGAGTCAGCAATCCCATGGCCTTTCTGTTAGTAACATACAGACACCATTTGATTAGGATTGATATTGTGTAGCTAGTCTG[C/T]
TGTACCCATTGTAGTAAACTGATGCTAAAAAGTCTGAAGTAGGCTAGTAAGTAAATAAGTAAATTTTACCACATAAAAGAATCCAGCCTCCCTGCAGGCA

Reverse complement sequence

TGCCTGCAGGGAGGCTGGATTCTTTTATGTGGTAAAATTTACTTATTTACTTACTAGCCTACTTCAGACTTTTTAGCATCAGTTTACTACAATGGGTACA[G/A]
CAGACTAGCTACACAATATCAATCCTAATCAAATGGTGTCTGTATGTTACTAACAGAAAGGCCATGGGATTGCTGACTCGCTAATGAAGCAAGTTAGGGA

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 62.90% 37.10% 0.02% 0.00% NA
All Indica  2759 95.90% 4.10% 0.00% 0.00% NA
All Japonica  1512 0.90% 99.10% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 95.00% 5.00% 0.00% 0.00% NA
Indica II  465 91.60% 8.40% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.50% 0.00% 0.00% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 43.30% 55.60% 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
vg0903407270 C -> T LOC_Os09g07010.1 upstream_gene_variant ; 4161.0bp to feature; MODIFIER silent_mutation Average:71.432; most accessible tissue: Callus, score: 81.654 N N N N
vg0903407270 C -> T LOC_Os09g07040.1 upstream_gene_variant ; 4956.0bp to feature; MODIFIER silent_mutation Average:71.432; most accessible tissue: Callus, score: 81.654 N N N N
vg0903407270 C -> T LOC_Os09g07030.1 downstream_gene_variant ; 1610.0bp to feature; MODIFIER silent_mutation Average:71.432; most accessible tissue: Callus, score: 81.654 N N N N
vg0903407270 C -> T LOC_Os09g07020.1 intron_variant ; MODIFIER silent_mutation Average:71.432; most accessible tissue: Callus, score: 81.654 N N N N
vg0903407270 C -> T LOC_Os09g07020.2 intron_variant ; MODIFIER silent_mutation Average:71.432; most accessible tissue: Callus, score: 81.654 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0903407270 NA 3.58E-07 mr1190 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
vg0903407270 NA 1.08E-08 mr1986 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