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Detailed information for vg1119511230:

Variant ID: vg1119511230 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19511230
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, T: 0.04, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


ATAAATTGATCGGCTAGGGAGTATATACCGTTTTTTATTTAGTCAATAGGTATATACTGTTTAGTATAGTAGCAGTAGTATATAGGAGTCACTAATACAG[A/T]
TCCTTCCATCTGTGACGGCCCATAACAAGACTGGAATTTGCGGGCCGTCACAAGGAAGTAATCTCAATCGGGCCAAAGTTTCGCCCGATTGAGATATGGT

Reverse complement sequence

ACCATATCTCAATCGGGCGAAACTTTGGCCCGATTGAGATTACTTCCTTGTGACGGCCCGCAAATTCCAGTCTTGTTATGGGCCGTCACAGATGGAAGGA[T/A]
CTGTATTAGTGACTCCTATATACTACTGCTACTATACTAAACAGTATATACCTATTGACTAAATAAAAAACGGTATATACTCCCTAGCCGATCAATTTAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.00% 7.30% 19.17% 4.51% NA
All Indica  2759 56.80% 7.80% 29.79% 5.58% NA
All Japonica  1512 89.50% 7.70% 1.39% 1.39% NA
Aus  269 75.50% 0.40% 12.27% 11.90% NA
Indica I  595 49.90% 4.70% 37.65% 7.73% NA
Indica II  465 36.60% 23.40% 32.69% 7.31% NA
Indica III  913 73.80% 1.40% 21.69% 3.07% NA
Indica Intermediate  786 54.20% 8.40% 31.55% 5.85% NA
Temperate Japonica  767 94.10% 2.50% 0.91% 2.48% NA
Tropical Japonica  504 88.30% 9.30% 1.98% 0.40% NA
Japonica Intermediate  241 77.20% 21.20% 1.66% 0.00% NA
VI/Aromatic  96 82.30% 0.00% 17.71% 0.00% NA
Intermediate  90 64.40% 14.40% 14.44% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1119511230 A -> T LOC_Os11g33010.1 upstream_gene_variant ; 990.0bp to feature; MODIFIER silent_mutation Average:24.829; most accessible tissue: Callus, score: 66.222 N N N N
vg1119511230 A -> T LOC_Os11g33000.1 downstream_gene_variant ; 1307.0bp to feature; MODIFIER silent_mutation Average:24.829; most accessible tissue: Callus, score: 66.222 N N N N
vg1119511230 A -> T LOC_Os11g33000-LOC_Os11g33010 intergenic_region ; MODIFIER silent_mutation Average:24.829; most accessible tissue: Callus, score: 66.222 N N N N
vg1119511230 A -> DEL N N silent_mutation Average:24.829; most accessible tissue: Callus, score: 66.222 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1119511230 NA 2.62E-06 mr1077 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
vg1119511230 6.09E-06 6.09E-06 mr1463 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
vg1119511230 9.05E-07 NA mr1570 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
vg1119511230 NA 3.04E-06 mr1648 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
vg1119511230 8.47E-07 8.47E-07 mr1655 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
vg1119511230 NA 1.78E-06 mr1712 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
vg1119511230 2.18E-07 2.18E-07 mr1761 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
vg1119511230 2.02E-06 2.02E-06 mr1770 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
vg1119511230 8.35E-06 8.35E-06 mr1876 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
vg1119511230 NA 2.74E-06 mr1961 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
vg1119511230 NA 2.80E-06 mr1359_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
vg1119511230 NA 4.34E-06 mr1359_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