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Detailed information for vg0407669199:

Variant ID: vg0407669199 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 7669199
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGTTAAACAATTGTAGCCGATTTGGATGCTTATTAGGAGAAACTTACTGGGATAGCAGGAGCGGCTGGTTGTTCTTCTTCCTCAACATGATGACTTCC[T/C]
ACAGTTGAAGGGGTCTGGTCACTTGACGATTGTTGAGCAGAAGGAGAAGGAGGAGGTGAAGGCTGAAAAGAATGCAAGTGTTAAGTAGAATCGGCTAAAA

Reverse complement sequence

TTTTAGCCGATTCTACTTAACACTTGCATTCTTTTCAGCCTTCACCTCCTCCTTCTCCTTCTGCTCAACAATCGTCAAGTGACCAGACCCCTTCAACTGT[A/G]
GGAAGTCATCATGTTGAGGAAGAAGAACAACCAGCCGCTCCTGCTATCCCAGTAAGTTTCTCCTAATAAGCATCCAAATCGGCTACAATTGTTTAACCTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.80% 0.30% 5.40% 42.47% NA
All Indica  2759 27.60% 0.50% 8.23% 63.68% NA
All Japonica  1512 99.10% 0.00% 0.07% 0.79% NA
Aus  269 22.30% 0.00% 1.86% 75.84% NA
Indica I  595 54.30% 0.00% 3.53% 42.18% NA
Indica II  465 25.40% 0.60% 9.03% 64.95% NA
Indica III  913 8.70% 0.70% 11.06% 79.63% NA
Indica Intermediate  786 30.80% 0.50% 8.02% 60.69% NA
Temperate Japonica  767 99.70% 0.00% 0.00% 0.26% NA
Tropical Japonica  504 98.80% 0.00% 0.20% 0.99% NA
Japonica Intermediate  241 97.90% 0.00% 0.00% 2.07% NA
VI/Aromatic  96 68.80% 1.00% 19.79% 10.42% NA
Intermediate  90 67.80% 2.20% 3.33% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0407669199 T -> C LOC_Os04g13750.1 synonymous_variant ; p.Val694Val; LOW synonymous_codon Average:10.929; most accessible tissue: Callus, score: 51.5 N N N N
vg0407669199 T -> C LOC_Os04g13750.1 synonymous_variant ; p.Val694Val; LOW nonsynonymous_codon ; V694A Average:10.929; most accessible tissue: Callus, score: 51.5 benign 0.212 TOLERATED 0.81
vg0407669199 T -> DEL LOC_Os04g13750.1 N frameshift_variant Average:10.929; most accessible tissue: Callus, score: 51.5 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0407669199 4.86E-06 NA mr1425 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
vg0407669199 NA 1.52E-07 mr1425 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
vg0407669199 NA 3.15E-06 mr1603 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
vg0407669199 NA 8.96E-07 mr1425_2 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