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Detailed information for vg1100141854:

Variant ID: vg1100141854 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 141854
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.66, T: 0.35, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


AAATGTGTTCTCTTTTTGGAGATTTAGTGCATTCACAGGCTGGTTGCACCTAAACTGTCAATTGGAGGCATGTTTACAACTCTTCTTTGCACATAACTCA[T/C]
TGGTACAAACTGAATTGATAGAATCGGCACCACTGGTATACCTATACTTCTTTTAAAAGAAGGCAATTGTGGTGTTCGCAGTGAATCTTCCTATTGCAGC

Reverse complement sequence

GCTGCAATAGGAAGATTCACTGCGAACACCACAATTGCCTTCTTTTAAAAGAAGTATAGGTATACCAGTGGTGCCGATTCTATCAATTCAGTTTGTACCA[A/G]
TGAGTTATGTGCAAAGAAGAGTTGTAAACATGCCTCCAATTGACAGTTTAGGTGCAACCAGCCTGTGAATGCACTAAATCTCCAAAAAGAGAACACATTT

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 55.90% 43.70% 0.21% 0.21% NA
All Indica  2759 87.00% 12.40% 0.25% 0.33% NA
All Japonica  1512 1.60% 98.40% 0.00% 0.00% NA
Aus  269 65.80% 33.80% 0.37% 0.00% NA
Indica I  595 98.30% 1.50% 0.00% 0.17% NA
Indica II  465 53.80% 45.60% 0.00% 0.65% NA
Indica III  913 94.90% 4.80% 0.11% 0.22% NA
Indica Intermediate  786 88.90% 9.90% 0.76% 0.38% NA
Temperate Japonica  767 1.40% 98.60% 0.00% 0.00% NA
Tropical Japonica  504 1.40% 98.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 15.60% 84.40% 0.00% 0.00% NA
Intermediate  90 26.70% 70.00% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1100141854 T -> DEL N N silent_mutation Average:37.325; most accessible tissue: Zhenshan97 flower, score: 57.454 N N N N
vg1100141854 T -> C LOC_Os11g01250.1 upstream_gene_variant ; 1536.0bp to feature; MODIFIER silent_mutation Average:37.325; most accessible tissue: Zhenshan97 flower, score: 57.454 N N N N
vg1100141854 T -> C LOC_Os11g01240.1 downstream_gene_variant ; 2895.0bp to feature; MODIFIER silent_mutation Average:37.325; most accessible tissue: Zhenshan97 flower, score: 57.454 N N N N
vg1100141854 T -> C LOC_Os11g01270.1 downstream_gene_variant ; 2311.0bp to feature; MODIFIER silent_mutation Average:37.325; most accessible tissue: Zhenshan97 flower, score: 57.454 N N N N
vg1100141854 T -> C LOC_Os11g01260.1 intron_variant ; MODIFIER silent_mutation Average:37.325; most accessible tissue: Zhenshan97 flower, score: 57.454 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1100141854 NA 5.04E-06 mr1032 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
vg1100141854 NA 1.20E-13 mr1478 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
vg1100141854 NA 5.37E-06 mr1478 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
vg1100141854 NA 8.74E-12 mr1609 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
vg1100141854 NA 6.55E-07 mr1835 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
vg1100141854 NA 4.10E-12 mr1889 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
vg1100141854 NA 7.06E-10 mr1896 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
vg1100141854 NA 2.67E-10 mr1903 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
vg1100141854 NA 5.82E-11 mr1904 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
vg1100141854 NA 8.33E-16 mr1907 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
vg1100141854 NA 1.95E-11 mr1934 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
vg1100141854 NA 6.79E-10 mr1935 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
vg1100141854 NA 1.24E-06 mr1332_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
vg1100141854 NA 3.11E-11 mr1520_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
vg1100141854 NA 2.85E-09 mr1835_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
vg1100141854 3.76E-06 1.29E-15 mr1889_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
vg1100141854 NA 1.29E-09 mr1896_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
vg1100141854 NA 9.97E-13 mr1904_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
vg1100141854 NA 9.62E-15 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
vg1100141854 NA 7.40E-12 mr1934_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