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Detailed information for vg0307963417:

Variant ID: vg0307963417 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 7963417
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


GATTTCTTCCATCCTGCAAGAACCCGTCTCTGGATGCATGGAAGAGCGGGGACTCGGCAGCTCGGTTTGTTGTTGGCCTCTCTGATTTTGTGGTGATCAT[G/T]
TTTCTTTCCCTCGTTGGCTTTGTGGTTGGAGTTTTTTTTTCGTTAAGTAGCTCTCCATAACCTGTGCTAGCTCCACCCTATGTAAATTCCAACCTCTTGG

Reverse complement sequence

CCAAGAGGTTGGAATTTACATAGGGTGGAGCTAGCACAGGTTATGGAGAGCTACTTAACGAAAAAAAAACTCCAACCACAAAGCCAACGAGGGAAAGAAA[C/A]
ATGATCACCACAAAATCAGAGAGGCCAACAACAAACCGAGCTGCCGAGTCCCCGCTCTTCCATGCATCCAGAGACGGGTTCTTGCAGGATGGAAGAAATC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 2.00% 0.47% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.50% 6.20% 1.32% 0.00% 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 85.80% 11.70% 2.48% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 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
vg0307963417 G -> T LOC_Os03g14642.1 upstream_gene_variant ; 3535.0bp to feature; MODIFIER silent_mutation Average:55.05; most accessible tissue: Callus, score: 74.621 N N N N
vg0307963417 G -> T LOC_Os03g14654.1 downstream_gene_variant ; 1747.0bp to feature; MODIFIER silent_mutation Average:55.05; most accessible tissue: Callus, score: 74.621 N N N N
vg0307963417 G -> T LOC_Os03g14642-LOC_Os03g14654 intergenic_region ; MODIFIER silent_mutation Average:55.05; most accessible tissue: Callus, score: 74.621 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0307963417 NA 7.83E-08 mr1210 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
vg0307963417 NA 1.69E-08 mr1305 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
vg0307963417 7.37E-08 7.37E-08 mr1409 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
vg0307963417 NA 1.86E-09 mr1585 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
vg0307963417 NA 2.59E-07 mr1586 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
vg0307963417 NA 8.45E-06 mr1765 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
vg0307963417 7.52E-06 7.52E-06 mr1166_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
vg0307963417 6.35E-07 1.57E-10 mr1305_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
vg0307963417 NA 1.01E-06 mr1409_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
vg0307963417 NA 4.61E-06 mr1559_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
vg0307963417 6.94E-06 7.92E-12 mr1585_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
vg0307963417 NA 3.33E-08 mr1765_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