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Detailed information for vg0216375201:

Variant ID: vg0216375201 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16375201
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: 232. )

Flanking Sequence (100 bp) in Reference Genome:


TCTGAGTGACGACGAAGGCGATGATGCTGGAAAACTTGGAGATAAAGGGGCGACTGGAAAACTACCGAAGCAAGCCAATCCGAAGAAGAAAACATCCAGT[C/T]
GTCCTATGCCGAAAATTAGGAAGTCTTCCAGGTACAAATCATATAACGATCTTCCTTGCATTGATGCTCACCCATCATGAAAATAATACTGATAGCACAA

Reverse complement sequence

TTGTGCTATCAGTATTATTTTCATGATGGGTGAGCATCAATGCAAGGAAGATCGTTATATGATTTGTACCTGGAAGACTTCCTAATTTTCGGCATAGGAC[G/A]
ACTGGATGTTTTCTTCTTCGGATTGGCTTGCTTCGGTAGTTTTCCAGTCGCCCCTTTATCTCCAAGTTTTCCAGCATCATCGCCTTCGTCGTCACTCAGA

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 95.30% 4.20% 0.53% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 85.80% 12.60% 1.52% 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 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 98.80% 0.50% 0.65% 0.00% NA
Tropical Japonica  504 63.30% 33.50% 3.17% 0.00% NA
Japonica Intermediate  241 91.70% 7.50% 0.83% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0216375201 C -> T LOC_Os02g27630.1 missense_variant ; p.Arg249Cys; MODERATE nonsynonymous_codon ; R249C Average:39.791; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 benign 0.467 DELETERIOUS 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0216375201 NA 1.06E-06 mr1583 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
vg0216375201 2.92E-08 4.54E-12 mr1850_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