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Detailed information for vg0406869782:

Variant ID: vg0406869782 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6869782
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCTCTTCCTATTCTTTTATGTTACCAAATTAAAAGCAAGAAAAGCTATAATTTTAGTATTAAGGTGACCATAATTTTAAATGTACATATCTAATTTCT[A/G]
TTCTATCTAAATTGTTCCTGTATTTATAATTAAATTGACAATTTTAGATCCAATGTTTTGCTATACATAAGTAATATGTCATTGTGGTCTTCTTAACGTC

Reverse complement sequence

GACGTTAAGAAGACCACAATGACATATTACTTATGTATAGCAAAACATTGGATCTAAAATTGTCAATTTAATTATAAATACAGGAACAATTTAGATAGAA[T/C]
AGAAATTAGATATGTACATTTAAAATTATGGTCACCTTAATACTAAAATTATAGCTTTTCTTGCTTTTAATTTGGTAACATAAAAGAATAGGAAGAGAAA

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 50.30% 6.30% 16.55% 26.83% NA
All Indica  2759 27.30% 9.80% 25.37% 37.48% NA
All Japonica  1512 99.30% 0.00% 0.07% 0.66% NA
Aus  269 2.20% 8.90% 23.05% 65.80% NA
Indica I  595 9.40% 10.60% 37.31% 42.69% NA
Indica II  465 22.20% 5.20% 24.95% 47.74% NA
Indica III  913 39.40% 11.70% 18.29% 30.56% NA
Indica Intermediate  786 29.90% 9.80% 24.81% 35.50% NA
Temperate Japonica  767 99.70% 0.00% 0.13% 0.13% NA
Tropical Japonica  504 99.20% 0.00% 0.00% 0.79% NA
Japonica Intermediate  241 97.90% 0.00% 0.00% 2.07% NA
VI/Aromatic  96 59.40% 2.10% 6.25% 32.29% NA
Intermediate  90 65.60% 2.20% 14.44% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0406869782 A -> DEL N N silent_mutation Average:36.68; most accessible tissue: Minghui63 young leaf, score: 57.221 N N N N
vg0406869782 A -> G LOC_Os04g12430.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:36.68; most accessible tissue: Minghui63 young leaf, score: 57.221 N N N N
vg0406869782 A -> G LOC_Os04g12430.1 5_prime_UTR_variant ; 1986.0bp to feature; MODIFIER silent_mutation Average:36.68; most accessible tissue: Minghui63 young leaf, score: 57.221 N N N N
vg0406869782 A -> G LOC_Os04g12440.1 upstream_gene_variant ; 4068.0bp to feature; MODIFIER silent_mutation Average:36.68; most accessible tissue: Minghui63 young leaf, score: 57.221 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406869782 3.23E-07 1.61E-07 mr1071 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
vg0406869782 NA 2.01E-06 mr1100 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
vg0406869782 NA 2.34E-08 mr1133 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
vg0406869782 8.33E-07 4.92E-07 mr1140 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
vg0406869782 NA 3.14E-06 mr1199 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
vg0406869782 NA 2.40E-06 mr1203 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
vg0406869782 NA 2.18E-07 mr1213 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
vg0406869782 NA 1.08E-06 mr1246 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
vg0406869782 NA 5.33E-06 mr1305 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
vg0406869782 3.76E-06 2.52E-07 mr1395 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
vg0406869782 NA 4.21E-06 mr1403 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
vg0406869782 NA 2.94E-06 mr1515 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
vg0406869782 6.58E-06 NA mr1613 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
vg0406869782 6.13E-06 1.07E-07 mr1613 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
vg0406869782 7.83E-06 7.44E-07 mr1618 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
vg0406869782 NA 6.45E-06 mr1665 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
vg0406869782 2.53E-06 2.53E-06 mr1724 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
vg0406869782 1.32E-07 1.32E-07 mr1777 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
vg0406869782 NA 5.49E-06 mr1846 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
vg0406869782 8.30E-06 NA mr1071_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
vg0406869782 5.01E-09 NA mr1071_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
vg0406869782 6.68E-07 NA mr1080_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
vg0406869782 NA 7.21E-06 mr1133_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
vg0406869782 5.94E-08 NA mr1203_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
vg0406869782 NA 2.97E-07 mr1212_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
vg0406869782 NA 4.77E-09 mr1379_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
vg0406869782 NA 1.82E-06 mr1559_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
vg0406869782 5.37E-06 NA mr1613_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
vg0406869782 7.84E-08 1.90E-08 mr1613_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
vg0406869782 7.59E-06 NA mr1619_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