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Detailed information for vg0504466784:

Variant ID: vg0504466784 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 4466784
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGAAGCCATTGAGAATCATGTTGGCCTTCTTTAACTCATCATCTCCACGCCCAAACTTCTTGAACAACAAGTATGGCATCAAATTCACGGCGGCACCTC[C/T]
ATCCACTAGGACCCTAGAGACCGGCTTCCCATCAATATGACCTTTGAGATAAAGAGGCTTCATATGACGGTTTGACTCATCGGGCTTCTCAAAAACCGCA

Reverse complement sequence

TGCGGTTTTTGAGAAGCCCGATGAGTCAAACCGTCATATGAAGCCTCTTTATCTCAAAGGTCATATTGATGGGAAGCCGGTCTCTAGGGTCCTAGTGGAT[G/A]
GAGGTGCCGCCGTGAATTTGATGCCATACTTGTTGTTCAAGAAGTTTGGGCGTGGAGATGATGAGTTAAAGAAGGCCAACATGATTCTCAATGGCTTCAA

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 94.50% 1.30% 4.15% 0.04% NA
All Indica  2759 90.90% 2.20% 6.89% 0.04% NA
All Japonica  1512 99.70% 0.00% 0.20% 0.07% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 85.90% 1.80% 12.10% 0.17% NA
Indica II  465 85.80% 4.70% 9.46% 0.00% NA
Indica III  913 95.40% 0.80% 3.83% 0.00% NA
Indica Intermediate  786 92.40% 2.70% 4.96% 0.00% NA
Temperate Japonica  767 99.60% 0.00% 0.26% 0.13% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 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
vg0504466784 C -> T LOC_Os05g08190.1 missense_variant ; p.Gly64Arg; MODERATE nonsynonymous_codon ; G64R Average:17.228; most accessible tissue: Callus, score: 45.891 benign 1.452 DELETERIOUS 0.01
vg0504466784 C -> DEL LOC_Os05g08190.1 N frameshift_variant Average:17.228; most accessible tissue: Callus, score: 45.891 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0504466784 4.62E-06 NA mr1679_2 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