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Detailed information for vg0729463054:

Variant ID: vg0729463054 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 29463054
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


AATAAAAAAGTATGTTGATAGAAGATGAACTGTATGGAGACAATCTAAACATCACCATGCAAGAGTAACAAAGTTATATGTGCCCGAATATTAGTGTTAT[C/T]
ATATTAGCCCAATTAATTGTATAGATAGAAATTGTGAAAGCTGGATGCTATACAACACCAACCCATCATAGGCATAAGAACATTGACATCAGGCCAAGTG

Reverse complement sequence

CACTTGGCCTGATGTCAATGTTCTTATGCCTATGATGGGTTGGTGTTGTATAGCATCCAGCTTTCACAATTTCTATCTATACAATTAATTGGGCTAATAT[G/A]
ATAACACTAATATTCGGGCACATATAACTTTGTTACTCTTGCATGGTGATGTTTAGATTGTCTCCATACAGTTCATCTTCTATCAACATACTTTTTTATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.90% 2.20% 0.83% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 90.80% 6.80% 2.38% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 83.30% 12.50% 4.17% 0.00% NA
Tropical Japonica  504 98.40% 0.80% 0.79% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 2.22% 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
vg0729463054 C -> T LOC_Os07g49200.1 upstream_gene_variant ; 3753.0bp to feature; MODIFIER silent_mutation Average:38.601; most accessible tissue: Callus, score: 50.835 N N N N
vg0729463054 C -> T LOC_Os07g49210.1 upstream_gene_variant ; 2119.0bp to feature; MODIFIER silent_mutation Average:38.601; most accessible tissue: Callus, score: 50.835 N N N N
vg0729463054 C -> T LOC_Os07g49200-LOC_Os07g49210 intergenic_region ; MODIFIER silent_mutation Average:38.601; most accessible tissue: Callus, score: 50.835 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0729463054 3.02E-06 9.78E-07 mr1332_2 Jap_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
vg0729463054 NA 3.77E-07 mr1354_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
vg0729463054 NA 8.53E-06 mr1829_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
vg0729463054 NA 9.66E-07 mr1902_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