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Detailed information for vg0316311631:

Variant ID: vg0316311631 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16311631
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.09, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


ACACATCCATAATTTTGGACTAATTCGCGAGACGAATCTATTGAATCTAATTAATCTATGATTAGCCTATGTGATGCTATAGTAAACATTCTCTAATTAT[G/A]
GATTAATTAGGCTTAAAAAATTTATCTTGCAAATTAGCTTTCATTTATGTAATTAGTTTTGTAAGTAGTCTATATTTAATAGTCTAAATTGGTGTCTAAA

Reverse complement sequence

TTTAGACACCAATTTAGACTATTAAATATAGACTACTTACAAAACTAATTACATAAATGAAAGCTAATTTGCAAGATAAATTTTTTAAGCCTAATTAATC[C/T]
ATAATTAGAGAATGTTTACTATAGCATCACATAGGCTAATCATAGATTAATTAGATTCAATAGATTCGTCTCGCGAATTAGTCCAAAATTATGGATGTGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.20% 48.80% 0.08% 0.00% NA
All Indica  2759 79.90% 20.00% 0.14% 0.00% NA
All Japonica  1512 1.30% 98.70% 0.00% 0.00% NA
Aus  269 53.90% 46.10% 0.00% 0.00% NA
Indica I  595 58.80% 41.20% 0.00% 0.00% NA
Indica II  465 95.70% 4.30% 0.00% 0.00% NA
Indica III  913 85.00% 15.00% 0.00% 0.00% NA
Indica Intermediate  786 80.50% 19.00% 0.51% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 2.60% 97.40% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 44.40% 55.60% 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
vg0316311631 G -> A LOC_Os03g28330.1 upstream_gene_variant ; 3999.0bp to feature; MODIFIER silent_mutation Average:61.316; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0316311631 G -> A LOC_Os03g28330.5 upstream_gene_variant ; 3999.0bp to feature; MODIFIER silent_mutation Average:61.316; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0316311631 G -> A LOC_Os03g28330-LOC_Os03g28350 intergenic_region ; MODIFIER silent_mutation Average:61.316; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316311631 NA 3.60E-13 mr1170 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
vg0316311631 2.54E-07 2.54E-07 mr1681 Ind_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
vg0316311631 NA 1.40E-14 mr1162_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
vg0316311631 NA 8.81E-08 mr1749_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
vg0316311631 NA 1.56E-10 mr1761_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