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Detailed information for vg0131498286:

Variant ID: vg0131498286 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 31498286
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


ATGAACTAATATGGCACAAAATCATCTACATGCTCGCTTCATAGACCCCTCTTGATAGTACGGCACCTATCTAGTAAATCCGGTCTACACCAAACACCAA[G/A]
ACCGGGAAAAAGACTAAGAAAACATTCTTAGCTCCATTATACCTTAGCCTTGCGCCATCCAACTTGGGGTCAATGCTTGAGCCAACATCAACACTTGTGA

Reverse complement sequence

TCACAAGTGTTGATGTTGGCTCAAGCATTGACCCCAAGTTGGATGGCGCAAGGCTAAGGTATAATGGAGCTAAGAATGTTTTCTTAGTCTTTTTCCCGGT[C/T]
TTGGTGTTTGGTGTAGACCGGATTTACTAGATAGGTGCCGTACTATCAAGAGGGGTCTATGAAGCGAGCATGTAGATGATTTTGTGCCATATTAGTTCAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 1.80% 0.32% 0.34% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.50% 5.60% 0.86% 1.06% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.10% 0.52% 0.26% NA
Tropical Japonica  504 81.50% 16.70% 1.39% 0.40% NA
Japonica Intermediate  241 94.20% 0.00% 0.83% 4.98% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 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
vg0131498286 G -> A LOC_Os01g54740.1 3_prime_UTR_variant ; 205.0bp to feature; MODIFIER silent_mutation Average:28.675; most accessible tissue: Zhenshan97 flower, score: 56.224 N N N N
vg0131498286 G -> A LOC_Os01g54750.1 upstream_gene_variant ; 4241.0bp to feature; MODIFIER silent_mutation Average:28.675; most accessible tissue: Zhenshan97 flower, score: 56.224 N N N N
vg0131498286 G -> DEL N N silent_mutation Average:28.675; most accessible tissue: Zhenshan97 flower, score: 56.224 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0131498286 2.67E-06 2.66E-06 mr1335_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
vg0131498286 NA 1.20E-07 mr1363_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