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Detailed information for vg0111834681:

Variant ID: vg0111834681 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 11834681
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.24, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AAGAGAGAAAAAGGCCGAAGAGCAAAGGGATAAAAGGTTCAATGAGTTGCGACCACCACCGGTATGGAGGCGTAAAACCATAGAGAAGGGAGAACCGGTT[A/G]
TTGTAGAGAAGAAGGAAGAACAATCGGTTGCTAAAGATGAGTCATCTCCAAAAGTAGACATGGATATCAACATGGTATGTATGTTGCCTATGGAGTTTTG

Reverse complement sequence

CAAAACTCCATAGGCAACATACATACCATGTTGATATCCATGTCTACTTTTGGAGATGACTCATCTTTAGCAACCGATTGTTCTTCCTTCTTCTCTACAA[T/C]
AACCGGTTCTCCCTTCTCTATGGTTTTACGCCTCCATACCGGTGGTGGTCGCAACTCATTGAACCTTTTATCCCTTTGCTCTTCGGCCTTTTTCTCTCTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.50% 32.60% 0.72% 0.11% NA
All Indica  2759 98.00% 1.30% 0.62% 0.07% NA
All Japonica  1512 4.00% 96.00% 0.00% 0.00% NA
Aus  269 92.20% 0.70% 5.95% 1.12% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 97.00% 2.80% 0.22% 0.00% NA
Indica III  913 98.80% 0.30% 0.77% 0.11% NA
Indica Intermediate  786 96.90% 1.80% 1.15% 0.13% NA
Temperate Japonica  767 2.20% 97.80% 0.00% 0.00% NA
Tropical Japonica  504 7.10% 92.90% 0.00% 0.00% NA
Japonica Intermediate  241 2.90% 97.10% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 62.20% 36.70% 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
vg0111834681 A -> G LOC_Os01g21210.1 intron_variant ; MODIFIER silent_mutation Average:39.926; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 N N N N
vg0111834681 A -> DEL N N silent_mutation Average:39.926; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0111834681 NA 5.96E-67 mr1027 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
vg0111834681 NA 1.58E-49 mr1154 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
vg0111834681 NA 9.27E-85 mr1504 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
vg0111834681 NA 4.76E-90 mr1517 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
vg0111834681 NA 2.00E-56 mr1594 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
vg0111834681 NA 2.12E-87 mr1672 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
vg0111834681 NA 1.16E-59 mr1711 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
vg0111834681 NA 6.94E-33 mr1733 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
vg0111834681 NA 3.23E-93 mr1758 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
vg0111834681 NA 2.39E-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
vg0111834681 NA 6.00E-39 mr1891 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
vg0111834681 NA 9.07E-16 mr1968 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
vg0111834681 1.36E-06 1.51E-102 mr1987 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
vg0111834681 NA 2.61E-08 mr1335_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
vg0111834681 NA 7.70E-24 mr1350_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
vg0111834681 NA 2.16E-64 mr1733_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