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Detailed information for vg0222318703:

Variant ID: vg0222318703 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22318703
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


CCTTTAGTTTGTTACTACTCCCTCCGTCCCGCAATATAAGAGATTTTCAGTTTTTGCTTGCAACGTTTGACCACTCGTCTTTTTTTGCAAATATAAAAAA[C/T]
GAAAAGTTGTGCTTAAAGTACTGTAGATAATAAAGTAAGTCACAAATAAAATAATTAATAATTTCAGAAAATTTTGAATAAGATGAGTGATCAAACGTTA

Reverse complement sequence

TAACGTTTGATCACTCATCTTATTCAAAATTTTCTGAAATTATTAATTATTTTATTTGTGACTTACTTTATTATCTACAGTACTTTAAGCACAACTTTTC[G/A]
TTTTTTATATTTGCAAAAAAAGACGAGTGGTCAAACGTTGCAAGCAAAAACTGAAAATCTCTTATATTGCGGGACGGAGGGAGTAGTAACAAACTAAAGG

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 90.20% 9.70% 0.08% 0.00% NA
All Indica  2759 97.20% 2.80% 0.00% 0.00% NA
All Japonica  1512 88.80% 11.00% 0.13% 0.00% NA
Aus  269 25.30% 74.00% 0.74% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 97.60% 2.40% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 4.10% 0.00% 0.00% NA
Temperate Japonica  767 81.10% 18.60% 0.26% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 90.50% 9.50% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0222318703 C -> T LOC_Os02g36950.1 downstream_gene_variant ; 1152.0bp to feature; MODIFIER silent_mutation Average:48.053; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0222318703 C -> T LOC_Os02g36950.2 downstream_gene_variant ; 1152.0bp to feature; MODIFIER silent_mutation Average:48.053; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0222318703 C -> T LOC_Os02g36940-LOC_Os02g36950 intergenic_region ; MODIFIER silent_mutation Average:48.053; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222318703 1.06E-07 NA mr1087_2 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
vg0222318703 NA 8.07E-10 mr1174_2 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
vg0222318703 NA 5.34E-06 mr1174_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
vg0222318703 NA 1.03E-09 mr1347_2 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