Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0335310118:

Variant ID: vg0335310118 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 35310118
Reference Allele: AAlternative Allele: T,G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.33, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:


CAAATCGACCTTTAATAAAATTTATTTTGAAAATAGACCCAAAATATTCCTTACTTCCCTAAATGTTTGACGCTGTTGACTTTTTAAAGTATGTTTAACC[A/T,G]
TTTGTCTTATTCAAAAACTTTTGTGAAATATGTAAAACTATATGTATATATAAAAGTATATTTAACAATAAATCAAATGATAGGAAAAGAATTAATTATT

Reverse complement sequence

AATAATTAATTCTTTTCCTATCATTTGATTTATTGTTAAATATACTTTTATATATACATATAGTTTTACATATTTCACAAAAGTTTTTGAATAAGACAAA[T/A,C]
GGTTAAACATACTTTAAAAAGTCAACAGCGTCAAACATTTAGGGAAGTAAGGAATATTTTGGGTCTATTTTCAAAATAAATTTTATTAAAGGTCGATTTG

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 64.60% 17.70% 0.17% 0.00% T: 17.52%
All Indica  2759 69.60% 1.10% 0.18% 0.00% T: 29.14%
All Japonica  1512 47.00% 52.60% 0.13% 0.00% T: 0.26%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 80.20% 1.30% 0.34% 0.00% T: 18.15%
Indica II  465 41.50% 2.40% 0.43% 0.00% T: 55.70%
Indica III  913 83.70% 0.40% 0.11% 0.00% T: 15.77%
Indica Intermediate  786 61.80% 0.90% 0.00% 0.00% T: 37.28%
Temperate Japonica  767 10.30% 89.20% 0.26% 0.00% T: 0.26%
Tropical Japonica  504 93.30% 6.30% 0.00% 0.00% T: 0.40%
Japonica Intermediate  241 66.80% 33.20% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 1.00% 0.00% 0.00% T: 1.04%
Intermediate  90 65.60% 12.20% 1.11% 0.00% T: 21.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0335310118 A -> T LOC_Os03g62330.1 3_prime_UTR_variant ; 191.0bp to feature; MODIFIER silent_mutation Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 N N N N
vg0335310118 A -> T LOC_Os03g62314.1 upstream_gene_variant ; 732.0bp to feature; MODIFIER silent_mutation Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 N N N N
vg0335310118 A -> T LOC_Os03g62340.1 downstream_gene_variant ; 2333.0bp to feature; MODIFIER silent_mutation Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 N N N N
vg0335310118 A -> G LOC_Os03g62330.1 3_prime_UTR_variant ; 191.0bp to feature; MODIFIER silent_mutation Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 N N N N
vg0335310118 A -> G LOC_Os03g62314.1 upstream_gene_variant ; 732.0bp to feature; MODIFIER silent_mutation Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 N N N N
vg0335310118 A -> G LOC_Os03g62340.1 downstream_gene_variant ; 2333.0bp to feature; MODIFIER silent_mutation Average:59.444; most accessible tissue: Minghui63 root, score: 79.74 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0335310118 NA 9.53E-06 mr1099 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
vg0335310118 NA 1.80E-06 mr1180 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
vg0335310118 NA 5.99E-06 mr1911 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
vg0335310118 NA 9.71E-07 mr1918 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
vg0335310118 NA 2.46E-08 mr1942 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
vg0335310118 NA 1.91E-07 mr1095_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
vg0335310118 NA 3.30E-07 mr1099_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
vg0335310118 NA 5.38E-07 mr1180_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
vg0335310118 NA 7.66E-07 mr1183_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
vg0335310118 NA 1.76E-06 mr1222_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
vg0335310118 NA 9.52E-07 mr1554_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
vg0335310118 NA 2.77E-06 mr1730_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
vg0335310118 NA 2.69E-08 mr1794_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
vg0335310118 NA 1.02E-09 mr1815_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
vg0335310118 NA 3.36E-12 mr1879_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
vg0335310118 NA 5.07E-11 mr1942_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
vg0335310118 NA 1.37E-06 mr1977_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