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Detailed information for vg0903404722:

Variant ID: vg0903404722 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 3404722
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, C: 0.10, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


AGGCTCTACGGCAGCATCGAAGTTTGACTGTAGCATTCAAAATTCAGAAAGAAAAGAAAGAACATGAGAAATCAACTTCACATAAACTATGTGTAGGATT[G/C]
AGACTAGAGATTAAGCAAGACATACCTCATAGAAGAATGCAACAGATACACGGTAGCGAGGGGAGTTGTTAACAACTCGATGAAGTGTTGGCTGATATAT

Reverse complement sequence

ATATATCAGCCAACACTTCATCGAGTTGTTAACAACTCCCCTCGCTACCGTGTATCTGTTGCATTCTTCTATGAGGTATGTCTTGCTTAATCTCTAGTCT[C/G]
AATCCTACACATAGTTTATGTGAAGTTGATTTCTCATGTTCTTTCTTTTCTTTCTGAATTTTGAATGCTACAGTCAAACTTCGATGCTGCCGTAGAGCCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.10% 37.90% 0.00% 0.02% NA
All Indica  2759 94.60% 5.40% 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 94.60% 5.40% 0.00% 0.00% NA
Indica II  465 91.80% 8.20% 0.00% 0.00% NA
Indica III  913 97.40% 2.60% 0.00% 0.00% NA
Indica Intermediate  786 93.00% 7.00% 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 42.20% 56.70% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0903404722 G -> DEL N N silent_mutation Average:71.79; most accessible tissue: Callus, score: 87.271 N N N N
vg0903404722 G -> C LOC_Os09g07010.1 upstream_gene_variant ; 1613.0bp to feature; MODIFIER silent_mutation Average:71.79; most accessible tissue: Callus, score: 87.271 N N N N
vg0903404722 G -> C LOC_Os09g07030.1 downstream_gene_variant ; 4158.0bp to feature; MODIFIER silent_mutation Average:71.79; most accessible tissue: Callus, score: 87.271 N N N N
vg0903404722 G -> C LOC_Os09g07020.1 intron_variant ; MODIFIER silent_mutation Average:71.79; most accessible tissue: Callus, score: 87.271 N N N N
vg0903404722 G -> C LOC_Os09g07020.2 intron_variant ; MODIFIER silent_mutation Average:71.79; most accessible tissue: Callus, score: 87.271 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0903404722 NA 1.16E-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
vg0903404722 NA 2.45E-10 mr1756_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