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Detailed information for vg0230671125:

Variant ID: vg0230671125 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 30671125
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.02, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AATTAGATAAGATTCAAATAGCACATAGCGTGGATTGTATGACACCTACTCCATAATACCATAAGTTGCTACATGTAACTGTGCAACTATTATAACTCCT[A/T]
TGGAAAGAAATTATTGTTTACAGTGTACTACACCTTGAATTTTCATTTATCGATTATTGAGAAGATGAGCCAATCTATAGTTGAGACAGTGGTTTTAATA

Reverse complement sequence

TATTAAAACCACTGTCTCAACTATAGATTGGCTCATCTTCTCAATAATCGATAAATGAAAATTCAAGGTGTAGTACACTGTAAACAATAATTTCTTTCCA[T/A]
AGGAGTTATAATAGTTGCACAGTTACATGTAGCAACTTATGGTATTATGGAGTAGGTGTCATACAATCCACGCTATGTGCTATTTGAATCTTATCTAATT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.70% 44.90% 0.08% 0.38% NA
All Indica  2759 83.80% 15.50% 0.11% 0.62% NA
All Japonica  1512 0.40% 99.60% 0.00% 0.00% NA
Aus  269 88.10% 11.50% 0.00% 0.37% NA
Indica I  595 93.40% 6.20% 0.00% 0.34% NA
Indica II  465 82.40% 16.80% 0.22% 0.65% NA
Indica III  913 75.60% 23.70% 0.00% 0.77% NA
Indica Intermediate  786 86.80% 12.30% 0.25% 0.64% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 0.00% 100.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 32.20% 66.70% 1.11% 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
vg0230671125 A -> T LOC_Os02g50240.1 downstream_gene_variant ; 3651.0bp to feature; MODIFIER silent_mutation Average:56.321; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0230671125 A -> T LOC_Os02g50240.2 downstream_gene_variant ; 3651.0bp to feature; MODIFIER silent_mutation Average:56.321; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0230671125 A -> T LOC_Os02g50230.1 intron_variant ; MODIFIER silent_mutation Average:56.321; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0230671125 A -> DEL N N silent_mutation Average:56.321; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0230671125 NA 1.13E-13 mr1070 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
vg0230671125 NA 3.45E-11 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
vg0230671125 NA 1.80E-07 mr1211 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
vg0230671125 NA 9.06E-13 mr1239 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
vg0230671125 NA 4.82E-07 mr1278 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
vg0230671125 NA 3.10E-12 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
vg0230671125 NA 3.86E-15 mr1386 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
vg0230671125 NA 2.80E-32 mr1414 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
vg0230671125 NA 3.43E-08 mr1442 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
vg0230671125 NA 5.27E-07 mr1680 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
vg0230671125 NA 2.20E-10 mr1683 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
vg0230671125 NA 1.58E-08 mr1776 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
vg0230671125 NA 1.23E-20 mr1838 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
vg0230671125 NA 2.80E-06 mr1881 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
vg0230671125 NA 2.03E-07 mr1979 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
vg0230671125 NA 1.38E-06 mr1090_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
vg0230671125 NA 8.94E-15 mr1128_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
vg0230671125 NA 2.06E-07 mr1211_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
vg0230671125 NA 8.16E-07 mr1498_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
vg0230671125 NA 3.02E-07 mr1951_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