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Detailed information for vg0301154652:

Variant ID: vg0301154652 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 1154652
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGAGGGGGAACAGTTTAAGAAAAAAGAACGAAGCAGCAACGTACCCAAAAAAAATATTCTTTCTAGGTTGATGGTTTTTTCTTGCTTCGATTTGCTTTGC[C/T]
TTTTTCTCTTGTGCTTAATTATAATTAAGTTTTCTTAGCTGCTCGATCTCTTCTTTGTGTCTGGGAGAAAATATATACTACTGGTACTAGTGATTAGGGG

Reverse complement sequence

CCCCTAATCACTAGTACCAGTAGTATATATTTTCTCCCAGACACAAAGAAGAGATCGAGCAGCTAAGAAAACTTAATTATAATTAAGCACAAGAGAAAAA[G/A]
GCAAAGCAAATCGAAGCAAGAAAAAACCATCAACCTAGAAAGAATATTTTTTTTGGGTACGTTGCTGCTTCGTTCTTTTTTCTTAAACTGTTCCCCCTCA

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 98.10% 1.80% 0.02% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 95.40% 4.60% 0.00% 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 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 88.50% 11.50% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 7.80% 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
vg0301154652 C -> T LOC_Os03g02900.1 3_prime_UTR_variant ; 336.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0301154652 NA 5.18E-07 mr1136 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