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Detailed information for vg0316520582:

Variant ID: vg0316520582 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16520582
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTGAGAAGTGCACGTTCGGAGTACCATCGAGCAAGCTGCTCGGGTTCCTCGTCTCTGGCAGAGAAATAAAAGCAAACCCTGAGAAGATCAAGGCAATC[G/A]
AGAACATGAAGTCGCCCACGAGACTCAAGAAAGTACAGAAGCTAACCGGATGCATGGCGGCACTAAGCAGGTTTGTCGCTAGGATGGGAGAACAAGGACA

Reverse complement sequence

TGTCCTTGTTCTCCCATCCTAGCGACAAACCTGCTTAGTGCCGCCATGCATCCGGTTAGCTTCTGTACTTTCTTGAGTCTCGTGGGCGACTTCATGTTCT[C/T]
GATTGCCTTGATCTTCTCAGGGTTTGCTTTTATTTCTCTGCCAGAGACGAGGAACCCGAGCAGCTTGCTCGATGGTACTCCGAACGTGCACTTCTCAGGA

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 52.30% 38.80% 1.25% 7.64% NA
All Indica  2759 74.20% 20.70% 0.72% 4.31% NA
All Japonica  1512 22.80% 63.10% 2.25% 11.84% NA
Aus  269 10.40% 68.80% 1.86% 18.96% NA
Indica I  595 60.00% 40.00% 0.00% 0.00% NA
Indica II  465 92.30% 6.00% 0.22% 1.51% NA
Indica III  913 75.70% 17.00% 1.42% 5.91% NA
Indica Intermediate  786 72.60% 19.20% 0.76% 7.38% NA
Temperate Japonica  767 1.60% 80.30% 2.61% 15.51% NA
Tropical Japonica  504 61.50% 31.20% 0.99% 6.35% NA
Japonica Intermediate  241 9.50% 75.10% 3.73% 11.62% NA
VI/Aromatic  96 5.20% 90.60% 0.00% 4.17% NA
Intermediate  90 48.90% 42.20% 0.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0316520582 G -> A LOC_Os03g29085.1 missense_variant ; p.Glu346Lys; MODERATE nonsynonymous_codon ; E346K Average:46.543; most accessible tissue: Minghui63 flag leaf, score: 64.284 benign 0.637 DELETERIOUS 0.04
vg0316520582 G -> DEL LOC_Os03g29085.1 N frameshift_variant Average:46.543; most accessible tissue: Minghui63 flag leaf, score: 64.284 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316520582 NA 1.56E-06 mr1130 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
vg0316520582 NA 1.83E-07 mr1542 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
vg0316520582 NA 2.18E-06 mr1077_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
vg0316520582 NA 8.63E-10 mr1093_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
vg0316520582 NA 5.19E-06 mr1123_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
vg0316520582 NA 2.71E-06 mr1206_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
vg0316520582 NA 1.42E-06 mr1220_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
vg0316520582 NA 1.36E-10 mr1235_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
vg0316520582 NA 1.73E-06 mr1243_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
vg0316520582 NA 9.18E-07 mr1248_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
vg0316520582 NA 5.03E-07 mr1250_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
vg0316520582 NA 7.36E-09 mr1251_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
vg0316520582 NA 1.36E-09 mr1423_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
vg0316520582 NA 8.33E-09 mr1435_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
vg0316520582 NA 1.47E-08 mr1542_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
vg0316520582 NA 9.81E-07 mr1596_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
vg0316520582 NA 4.70E-08 mr1599_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
vg0316520582 NA 9.13E-06 mr1736_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
vg0316520582 NA 5.30E-07 mr1739_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
vg0316520582 NA 4.74E-06 mr1936_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