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Detailed information for vg0301975407:

Variant ID: vg0301975407 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 1975407
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 130. )

Flanking Sequence (100 bp) in Reference Genome:


AGCACTTATGGCTAATCATGGACTAATTAGGCTCAAAAGATTCGTCTCGCGATATCCATGCAAACTGTGCAATTAGTTTTTGTTTTTATCTATATTTAAT[G/A]
CTCCATGCATGTATCCAAAGATTTGATGTGACGTTTTTGGGGGAAAAAAATTTTGAGAACTAAACCAAGCCTGAATAGATTCATACGGTTTTGTTGAAAA

Reverse complement sequence

TTTTCAACAAAACCGTATGAATCTATTCAGGCTTGGTTTAGTTCTCAAAATTTTTTTCCCCCAAAAACGTCACATCAAATCTTTGGATACATGCATGGAG[C/T]
ATTAAATATAGATAAAAACAAAAACTAATTGCACAGTTTGCATGGATATCGCGAGACGAATCTTTTGAGCCTAATTAGTCCATGATTAGCCATAAGTGCT

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 95.00% 5.00% 0.04% 0.00% NA
All Indica  2759 91.50% 8.40% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 73.40% 26.60% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.10% 0.22% 0.00% NA
Indica Intermediate  786 90.70% 9.30% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 98.90% 1.10% 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
vg0301975407 G -> A LOC_Os03g04300.3 downstream_gene_variant ; 780.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301975407 G -> A LOC_Os03g04300.2 downstream_gene_variant ; 804.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301975407 G -> A LOC_Os03g04300.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0301975407 NA 5.26E-06 mr1533 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
vg0301975407 NA 4.54E-06 mr1980 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
vg0301975407 6.07E-06 1.10E-08 mr1533_2 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