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Detailed information for vg0529442914:

Variant ID: vg0529442914 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 29442914
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


GTCACAACACGATCTCGGAAGGGAGACTCAGAATGCCTATTGAGTATACTTACATTGATGGCAGCGTCACGTTCGGCCGCCCCCTTCTCACAAAGGGGAA[C/T]
AGGGATGTTACTCGCCGTTGTCGGGCCACTGATCATCACCTGGCCGACACGACGTCCCATGGTTTCGCTGTTCAGACCTATGAATCGAGAACCAAATTTC

Reverse complement sequence

GAAATTTGGTTCTCGATTCATAGGTCTGAACAGCGAAACCATGGGACGTCGTGTCGGCCAGGTGATGATCAGTGGCCCGACAACGGCGAGTAACATCCCT[G/A]
TTCCCCTTTGTGAGAAGGGGGCGGCCGAACGTGACGCTGCCATCAATGTAAGTATACTCAATAGGCATTCTGAGTCTCCCTTCCGAGATCGTGTTGTGAC

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 88.60% 11.30% 0.11% 0.00% NA
All Indica  2759 81.20% 18.60% 0.18% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.60% 2.40% 0.00% 0.00% NA
Indica II  465 91.60% 8.40% 0.00% 0.00% NA
Indica III  913 66.20% 33.30% 0.55% 0.00% NA
Indica Intermediate  786 80.20% 19.80% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 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 85.60% 14.40% 0.00% 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
vg0529442914 C -> T LOC_Os05g51330.1 missense_variant ; p.Val223Ile; MODERATE nonsynonymous_codon ; V223I Average:41.505; most accessible tissue: Minghui63 panicle, score: 62.157 benign 1.402 TOLERATED 0.18

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0529442914 2.84E-07 NA mr1989 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
vg0529442914 7.31E-06 NA mr1989 Ind_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