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Detailed information for vg0232958327:

Variant ID: vg0232958327 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 32958327
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TTTAGCAACACATCCTAGCAGACAAGTTGGAGATTGACTTTTACATATTTGTCTTAGTAGCAAACGTCTCCAGGAGTAAAAATCGATGCAAAATCATTAT[T/C]
GAGTAATTTATTAGTACTGTCTTCTTATTCGGTTACTTTGTTCTATTGGCAGGTTATACTGGGCTTTCCTCCTGATAAACTCGTTCTAAAGACATTCGGT

Reverse complement sequence

ACCGAATGTCTTTAGAACGAGTTTATCAGGAGGAAAGCCCAGTATAACCTGCCAATAGAACAAAGTAACCGAATAAGAAGACAGTACTAATAAATTACTC[A/G]
ATAATGATTTTGCATCGATTTTTACTCCTGGAGACGTTTGCTACTAAGACAAATATGTAAAAGTCAATCTCCAACTTGTCTGCTAGGATGTGTTGCTAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.50% 29.90% 0.40% 0.25% NA
All Indica  2759 98.80% 1.00% 0.00% 0.25% NA
All Japonica  1512 10.80% 87.90% 1.12% 0.13% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.40% 2.20% 0.00% 0.43% NA
Indica III  913 99.00% 0.80% 0.00% 0.22% NA
Indica Intermediate  786 98.50% 1.10% 0.00% 0.38% NA
Temperate Japonica  767 20.20% 77.60% 2.22% 0.00% NA
Tropical Japonica  504 0.00% 99.80% 0.00% 0.20% NA
Japonica Intermediate  241 3.70% 95.90% 0.00% 0.41% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 50.00% 44.40% 2.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0232958327 T -> DEL N N silent_mutation Average:41.686; most accessible tissue: Zhenshan97 flower, score: 59.202 N N N N
vg0232958327 T -> C LOC_Os02g53800.1 upstream_gene_variant ; 2372.0bp to feature; MODIFIER silent_mutation Average:41.686; most accessible tissue: Zhenshan97 flower, score: 59.202 N N N N
vg0232958327 T -> C LOC_Os02g53820.1 upstream_gene_variant ; 3635.0bp to feature; MODIFIER silent_mutation Average:41.686; most accessible tissue: Zhenshan97 flower, score: 59.202 N N N N
vg0232958327 T -> C LOC_Os02g53820.2 upstream_gene_variant ; 3635.0bp to feature; MODIFIER silent_mutation Average:41.686; most accessible tissue: Zhenshan97 flower, score: 59.202 N N N N
vg0232958327 T -> C LOC_Os02g53790.1 downstream_gene_variant ; 3241.0bp to feature; MODIFIER silent_mutation Average:41.686; most accessible tissue: Zhenshan97 flower, score: 59.202 N N N N
vg0232958327 T -> C LOC_Os02g53790.2 downstream_gene_variant ; 3252.0bp to feature; MODIFIER silent_mutation Average:41.686; most accessible tissue: Zhenshan97 flower, score: 59.202 N N N N
vg0232958327 T -> C LOC_Os02g53810.1 intron_variant ; MODIFIER silent_mutation Average:41.686; most accessible tissue: Zhenshan97 flower, score: 59.202 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0232958327 NA 4.31E-10 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0232958327 NA 4.09E-13 mr1035 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
vg0232958327 NA 1.43E-16 mr1062 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
vg0232958327 NA 2.07E-10 mr1322 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
vg0232958327 NA 1.60E-10 mr1336 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
vg0232958327 NA 2.88E-12 mr1449 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
vg0232958327 NA 3.92E-12 mr1579 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
vg0232958327 NA 2.13E-08 mr1585 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
vg0232958327 NA 1.67E-10 mr1623 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
vg0232958327 NA 9.67E-12 mr1626 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
vg0232958327 NA 4.27E-08 mr1648 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
vg0232958327 NA 2.20E-13 mr1701 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
vg0232958327 NA 2.40E-18 mr1715 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
vg0232958327 NA 1.79E-11 mr1905 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
vg0232958327 NA 4.03E-09 mr1022_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
vg0232958327 NA 1.47E-08 mr1030_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
vg0232958327 NA 5.95E-14 mr1035_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
vg0232958327 NA 3.79E-20 mr1062_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
vg0232958327 NA 7.65E-06 mr1164_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
vg0232958327 NA 2.97E-15 mr1324_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
vg0232958327 NA 1.50E-12 mr1325_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
vg0232958327 NA 3.83E-19 mr1336_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
vg0232958327 NA 4.05E-16 mr1342_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
vg0232958327 NA 4.89E-21 mr1383_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
vg0232958327 NA 7.00E-25 mr1484_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
vg0232958327 3.13E-06 3.13E-06 mr1571_2 Jap_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
vg0232958327 NA 7.42E-08 mr1576_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
vg0232958327 NA 9.28E-13 mr1666_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
vg0232958327 NA 3.40E-09 mr1705_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
vg0232958327 NA 5.15E-08 mr1709_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
vg0232958327 NA 2.94E-07 mr1748_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
vg0232958327 NA 7.78E-08 mr1749_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
vg0232958327 NA 4.83E-13 mr1761_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
vg0232958327 NA 7.27E-10 mr1765_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
vg0232958327 NA 3.10E-20 mr1817_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
vg0232958327 NA 4.31E-08 mr1821_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
vg0232958327 NA 5.24E-20 mr1945_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