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Detailed information for vg0403206982:

Variant ID: vg0403206982 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 3206982
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TGCTGGGGTGCACACCATCGGCGCGTTCTTCACCGTTGCTGCCCTCGCCTGTCGTGCGGGTGCCAGTCCTGGTGTAGACCATCTGGAGGAAGAGCAGACG[G/A]
GGAAACGGAGAAAAACAGATGCTCAAGAACTAAGCTTTATTATATAGGAATTTAAACTGCAATTGTTCTGTTCTGAATTAAAACACTTAAAAAGCAAGCA

Reverse complement sequence

TGCTTGCTTTTTAAGTGTTTTAATTCAGAACAGAACAATTGCAGTTTAAATTCCTATATAATAAAGCTTAGTTCTTGAGCATCTGTTTTTCTCCGTTTCC[C/T]
CGTCTGCTCTTCCTCCAGATGGTCTACACCAGGACTGGCACCCGCACGACAGGCGAGGGCAGCAACGGTGAAGAACGCGCCGATGGTGTGCACCCCAGCA

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 61.70% 18.60% 11.38% 8.40% NA
All Indica  2759 54.70% 22.40% 14.50% 8.41% NA
All Japonica  1512 66.30% 15.40% 7.87% 10.38% NA
Aus  269 98.10% 1.10% 0.37% 0.37% NA
Indica I  595 79.20% 0.80% 14.29% 5.71% NA
Indica II  465 57.00% 17.40% 16.99% 8.60% NA
Indica III  913 34.80% 43.60% 12.49% 9.09% NA
Indica Intermediate  786 57.90% 17.00% 15.52% 9.54% NA
Temperate Japonica  767 93.90% 1.80% 2.09% 2.22% NA
Tropical Japonica  504 31.00% 33.70% 14.88% 20.44% NA
Japonica Intermediate  241 52.70% 20.30% 11.62% 15.35% NA
VI/Aromatic  96 74.00% 13.50% 10.42% 2.08% NA
Intermediate  90 74.40% 11.10% 8.89% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0403206982 G -> DEL N N silent_mutation Average:26.514; most accessible tissue: Minghui63 young leaf, score: 56.213 N N N N
vg0403206982 G -> A LOC_Os04g06144.1 upstream_gene_variant ; 901.0bp to feature; MODIFIER silent_mutation Average:26.514; most accessible tissue: Minghui63 young leaf, score: 56.213 N N N N
vg0403206982 G -> A LOC_Os04g06160.1 downstream_gene_variant ; 230.0bp to feature; MODIFIER silent_mutation Average:26.514; most accessible tissue: Minghui63 young leaf, score: 56.213 N N N N
vg0403206982 G -> A LOC_Os04g06144-LOC_Os04g06160 intergenic_region ; MODIFIER silent_mutation Average:26.514; most accessible tissue: Minghui63 young leaf, score: 56.213 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0403206982 NA 8.86E-11 mr1026 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
vg0403206982 NA 1.88E-06 mr1076 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
vg0403206982 NA 5.07E-07 mr1082 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
vg0403206982 NA 3.02E-06 mr1083 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
vg0403206982 NA 7.74E-06 mr1113 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
vg0403206982 NA 4.05E-07 mr1116 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
vg0403206982 9.83E-07 4.02E-15 mr1118 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
vg0403206982 NA 1.09E-10 mr1161 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
vg0403206982 NA 5.30E-07 mr1247 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
vg0403206982 5.06E-06 NA mr1495 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
vg0403206982 1.89E-07 4.88E-18 mr1495 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
vg0403206982 NA 6.11E-06 mr1496 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
vg0403206982 NA 8.18E-10 mr1794 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
vg0403206982 NA 9.48E-08 mr1794 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
vg0403206982 NA 4.35E-08 mr1113_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
vg0403206982 NA 3.89E-08 mr1114_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
vg0403206982 NA 2.99E-07 mr1117_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
vg0403206982 NA 6.65E-14 mr1118_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
vg0403206982 NA 1.78E-06 mr1119_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
vg0403206982 NA 1.59E-09 mr1120_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
vg0403206982 NA 2.25E-06 mr1121_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
vg0403206982 NA 3.51E-09 mr1161_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
vg0403206982 NA 2.18E-09 mr1247_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
vg0403206982 NA 1.05E-06 mr1258_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
vg0403206982 NA 8.76E-15 mr1495_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
vg0403206982 NA 8.95E-11 mr1794_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
vg0403206982 NA 2.53E-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
vg0403206982 NA 1.35E-07 mr1961_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