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Detailed information for vg0216160657:

Variant ID: vg0216160657 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16160657
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.22, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


CATTCTTCTTCAAATATTTCATGTATCTTTCCTCCCAAAACCAAAAGTTACACCCAGATCCATCTTTCTACACCATTAAGAACAAATGTCACCTCAAACT[G/A]
AACTCAACACCACAACACACCAAATTCAATCAACTATTGCTCACCTCGTGGTCAGGGCAAGTGTAGAAAATGCGATCTGGATTACTAGCTGTCTTCGATG

Reverse complement sequence

CATCGAAGACAGCTAGTAATCCAGATCGCATTTTCTACACTTGCCCTGACCACGAGGTGAGCAATAGTTGATTGAATTTGGTGTGTTGTGGTGTTGAGTT[C/T]
AGTTTGAGGTGACATTTGTTCTTAATGGTGTAGAAAGATGGATCTGGGTGTAACTTTTGGTTTTGGGAGGAAAGATACATGAAATATTTGAAGAAGAATG

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 61.80% 37.80% 0.21% 0.15% NA
All Indica  2759 93.80% 5.80% 0.11% 0.22% NA
All Japonica  1512 1.40% 98.40% 0.13% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 88.80% 10.80% 0.00% 0.43% NA
Indica III  913 92.20% 7.70% 0.00% 0.11% NA
Indica Intermediate  786 94.30% 5.20% 0.13% 0.38% NA
Temperate Japonica  767 1.00% 98.80% 0.13% 0.00% NA
Tropical Japonica  504 1.40% 98.40% 0.20% 0.00% NA
Japonica Intermediate  241 2.50% 97.10% 0.00% 0.41% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 43.30% 51.10% 5.56% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0216160657 G -> A LOC_Os02g27420.1 downstream_gene_variant ; 527.0bp to feature; MODIFIER silent_mutation Average:49.061; most accessible tissue: Zhenshan97 young leaf, score: 74.302 N N N N
vg0216160657 G -> A LOC_Os02g27430.1 intron_variant ; MODIFIER silent_mutation Average:49.061; most accessible tissue: Zhenshan97 young leaf, score: 74.302 N N N N
vg0216160657 G -> DEL N N silent_mutation Average:49.061; most accessible tissue: Zhenshan97 young leaf, score: 74.302 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0216160657 NA 9.29E-56 mr1019 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
vg0216160657 NA 2.27E-39 mr1082 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
vg0216160657 NA 9.30E-47 mr1092 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
vg0216160657 NA 5.93E-10 mr1128 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
vg0216160657 NA 1.18E-67 mr1132 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
vg0216160657 NA 5.37E-75 mr1135 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
vg0216160657 NA 1.09E-45 mr1152 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
vg0216160657 NA 1.39E-50 mr1154 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
vg0216160657 NA 8.64E-88 mr1504 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
vg0216160657 NA 2.33E-30 mr1546 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
vg0216160657 NA 6.27E-37 mr1670 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
vg0216160657 NA 8.52E-60 mr1711 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
vg0216160657 NA 7.92E-34 mr1733 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
vg0216160657 NA 2.40E-19 mr1767 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
vg0216160657 NA 1.41E-28 mr1922 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
vg0216160657 NA 1.30E-103 mr1987 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
vg0216160657 NA 1.66E-35 mr1082_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
vg0216160657 NA 5.23E-16 mr1416_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