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Detailed information for vg0318126392:

Variant ID: vg0318126392 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18126392
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.07, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


ATAAACTAGTCTCAAATTTTCAAATTTATTTTTGCATACGGCTTCTTAAGTTACCCGTATGGAAAAATTGATTTTTCCATGTGGGTCCTTAAGTGGTCCA[C/T]
GTACAAACAAATGAAAAAAATTCAATTCTGAAAAATAATCACTCGAATTTTTAAAAACTTTCAATTGAAATGTTCAACCCAAAATTTAAAATATTCAACC

Reverse complement sequence

GGTTGAATATTTTAAATTTTGGGTTGAACATTTCAATTGAAAGTTTTTAAAAATTCGAGTGATTATTTTTCAGAATTGAATTTTTTTCATTTGTTTGTAC[G/A]
TGGACCACTTAAGGACCCACATGGAAAAATCAATTTTTCCATACGGGTAACTTAAGAAGCCGTATGCAAAAATAAATTTGAAAATTTGAGACTAGTTTAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.60% 31.10% 10.75% 2.48% NA
All Indica  2759 76.40% 2.50% 17.14% 3.95% NA
All Japonica  1512 14.30% 84.10% 1.52% 0.13% NA
Aus  269 90.30% 7.10% 1.49% 1.12% NA
Indica I  595 83.90% 2.40% 8.74% 5.04% NA
Indica II  465 64.70% 3.40% 26.45% 5.38% NA
Indica III  913 80.00% 1.20% 16.10% 2.74% NA
Indica Intermediate  786 73.70% 3.40% 19.21% 3.69% NA
Temperate Japonica  767 0.10% 99.70% 0.00% 0.13% NA
Tropical Japonica  504 39.10% 60.30% 0.40% 0.20% NA
Japonica Intermediate  241 7.50% 83.80% 8.71% 0.00% NA
VI/Aromatic  96 22.90% 76.00% 0.00% 1.04% NA
Intermediate  90 43.30% 45.60% 8.89% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0318126392 C -> T LOC_Os03g31730.1 intron_variant ; MODIFIER silent_mutation Average:17.541; most accessible tissue: Callus, score: 27.038 N N N N
vg0318126392 C -> DEL N N silent_mutation Average:17.541; most accessible tissue: Callus, score: 27.038 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318126392 NA 8.70E-10 mr1198 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
vg0318126392 NA 6.26E-07 mr1215 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
vg0318126392 NA 8.48E-08 mr1217 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
vg0318126392 NA 8.49E-15 mr1218 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
vg0318126392 NA 5.97E-09 mr1275 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
vg0318126392 NA 5.85E-10 mr1307 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
vg0318126392 NA 2.85E-09 mr1352 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
vg0318126392 NA 3.36E-06 mr1450 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
vg0318126392 NA 7.34E-09 mr1575 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
vg0318126392 4.04E-07 1.40E-13 mr1750 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
vg0318126392 NA 7.54E-07 mr1830 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
vg0318126392 NA 6.94E-07 mr1845 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
vg0318126392 NA 8.26E-07 mr1850 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
vg0318126392 NA 1.41E-08 mr1852 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
vg0318126392 6.56E-08 6.55E-08 mr1987 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
vg0318126392 NA 5.83E-09 mr1136_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
vg0318126392 NA 7.06E-16 mr1750_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
vg0318126392 NA 1.83E-08 mr1800_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
vg0318126392 NA 7.09E-08 mr1987_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