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Detailed information for vg0231596229:

Variant ID: vg0231596229 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 31596229
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


ACGGTTAAGCGCTAATTGCAGGGTTAAGCGTTTTTCGATTTGGCGACGGTTAAGCGCTAATTGGGAGGGTTAAGCGCTAATTGTAACTAAACAACTTGTG[C/T]
TTTTTATATTAGTGTAAACAACTTGTGCTTTTTATATTAGTGTAGATGAAGTCGGCTTGGGAATTTCAAATTTCCAATTGCACAATTGCACTGCCTTCTC

Reverse complement sequence

GAGAAGGCAGTGCAATTGTGCAATTGGAAATTTGAAATTCCCAAGCCGACTTCATCTACACTAATATAAAAAGCACAAGTTGTTTACACTAATATAAAAA[G/A]
CACAAGTTGTTTAGTTACAATTAGCGCTTAACCCTCCCAATTAGCGCTTAACCGTCGCCAAATCGAAAAACGCTTAACCCTGCAATTAGCGCTTAACCGT

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 58.80% 41.10% 0.08% 0.00% NA
All Indica  2759 31.00% 68.90% 0.11% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 94.80% 5.20% 0.00% 0.00% NA
Indica I  595 2.40% 97.50% 0.17% 0.00% NA
Indica II  465 51.20% 48.60% 0.22% 0.00% NA
Indica III  913 31.70% 68.30% 0.00% 0.00% NA
Indica Intermediate  786 39.80% 60.10% 0.13% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 77.80% 21.10% 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
vg0231596229 C -> T LOC_Os02g51580.1 upstream_gene_variant ; 1103.0bp to feature; MODIFIER silent_mutation Average:60.933; most accessible tissue: Callus, score: 88.732 N N N N
vg0231596229 C -> T LOC_Os02g51590.1 upstream_gene_variant ; 1395.0bp to feature; MODIFIER silent_mutation Average:60.933; most accessible tissue: Callus, score: 88.732 N N N N
vg0231596229 C -> T LOC_Os02g51570.1 downstream_gene_variant ; 3077.0bp to feature; MODIFIER silent_mutation Average:60.933; most accessible tissue: Callus, score: 88.732 N N N N
vg0231596229 C -> T LOC_Os02g51580-LOC_Os02g51590 intergenic_region ; MODIFIER silent_mutation Average:60.933; most accessible tissue: Callus, score: 88.732 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0231596229 NA 4.72E-12 Grain_thickness Ind_All YES 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
vg0231596229 NA 2.30E-06 Grain_weight Ind_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
vg0231596229 NA 4.56E-13 mr1531 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
vg0231596229 NA 7.60E-23 mr1598 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
vg0231596229 NA 3.58E-06 mr1598 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
vg0231596229 NA 3.88E-10 mr1712 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
vg0231596229 NA 1.43E-08 mr1717 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
vg0231596229 NA 1.83E-08 mr1770 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
vg0231596229 NA 2.36E-08 mr1946 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
vg0231596229 NA 5.33E-06 mr1123_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
vg0231596229 NA 2.83E-08 mr1124_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
vg0231596229 NA 5.05E-07 mr1227_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
vg0231596229 NA 1.66E-06 mr1272_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
vg0231596229 NA 8.69E-07 mr1321_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
vg0231596229 NA 6.79E-09 mr1478_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
vg0231596229 NA 4.54E-19 mr1531_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
vg0231596229 NA 8.67E-06 mr1655_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
vg0231596229 NA 2.27E-14 mr1717_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
vg0231596229 NA 1.08E-06 mr1717_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
vg0231596229 NA 9.28E-08 mr1722_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
vg0231596229 NA 8.99E-14 mr1728_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
vg0231596229 NA 2.11E-08 mr1907_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
vg0231596229 NA 3.14E-07 mr1910_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
vg0231596229 NA 3.95E-09 mr1946_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
vg0231596229 NA 3.95E-09 mr1948_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