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Detailed information for vg0907093222:

Variant ID: vg0907093222 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7093222
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.59, G: 0.42, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


GTCTATGTTTGTAAAATTATAATTATTTTAAATTTATTATCAGTAATATAATTATGTTCTCACATATACATGGAAAAAGGTGGGAAGGAGAGAGAAGCGG[T/G]
TGTATTTTTTAAATTGATGTATATAATTTGTGTTTTTATGTTTTTTCTGTAATCTACTTTTATTATAGTACGTTATGTATGTACTTGGTATTTTGGGCTT

Reverse complement sequence

AAGCCCAAAATACCAAGTACATACATAACGTACTATAATAAAAGTAGATTACAGAAAAAACATAAAAACACAAATTATATACATCAATTTAAAAAATACA[A/C]
CCGCTTCTCTCTCCTTCCCACCTTTTTCCATGTATATGTGAGAACATAATTATATTACTGATAATAAATTTAAAATAATTATAATTTTACAAACATAGAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.60% 30.80% 0.06% 10.56% NA
All Indica  2759 87.20% 1.20% 0.04% 11.49% NA
All Japonica  1512 1.70% 86.70% 0.13% 11.44% NA
Aus  269 98.10% 0.70% 0.00% 1.12% NA
Indica I  595 97.00% 0.70% 0.17% 2.18% NA
Indica II  465 96.10% 0.90% 0.00% 3.01% NA
Indica III  913 71.30% 0.80% 0.00% 27.93% NA
Indica Intermediate  786 93.10% 2.40% 0.00% 4.45% NA
Temperate Japonica  767 1.00% 96.60% 0.26% 2.09% NA
Tropical Japonica  504 2.00% 83.50% 0.00% 14.48% NA
Japonica Intermediate  241 3.30% 61.80% 0.00% 34.85% NA
VI/Aromatic  96 34.40% 65.60% 0.00% 0.00% NA
Intermediate  90 42.20% 51.10% 0.00% 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
vg0907093222 T -> G LOC_Os09g12410.1 upstream_gene_variant ; 2429.0bp to feature; MODIFIER silent_mutation Average:26.64; most accessible tissue: Callus, score: 46.827 N N N N
vg0907093222 T -> G LOC_Os09g12400.1 downstream_gene_variant ; 836.0bp to feature; MODIFIER silent_mutation Average:26.64; most accessible tissue: Callus, score: 46.827 N N N N
vg0907093222 T -> G LOC_Os09g12390-LOC_Os09g12400 intergenic_region ; MODIFIER silent_mutation Average:26.64; most accessible tissue: Callus, score: 46.827 N N N N
vg0907093222 T -> DEL N N silent_mutation Average:26.64; most accessible tissue: Callus, score: 46.827 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907093222 NA 8.01E-26 mr1024 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
vg0907093222 NA 5.50E-10 mr1128 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
vg0907093222 NA 2.59E-36 mr1542 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
vg0907093222 5.97E-07 4.03E-07 mr1693 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
vg0907093222 NA 2.98E-08 mr1299_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
vg0907093222 NA 3.52E-14 mr1333_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
vg0907093222 NA 1.53E-11 mr1537_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
vg0907093222 NA 1.07E-08 mr1600_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
vg0907093222 NA 3.65E-08 mr1700_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
vg0907093222 NA 2.02E-07 mr1727_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
vg0907093222 NA 1.13E-07 mr1783_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
vg0907093222 NA 9.87E-08 mr1804_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
vg0907093222 NA 2.41E-35 mr1888_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