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Detailed information for vg0902272767:

Variant ID: vg0902272767 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 2272767
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.55, C: 0.43, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:


TGAACATGATGATGCAACAACTCCAGAACCAACAAAACCAGGGGAACAATCATGCTCCTCCCCAGAACAAGTTAGCAGAATTTCTTCGTGTGAGGCCGCC[T/C]
ACTTTTTCCAGTACTACCAATCCAGTTGAGGCTGGTGATTGGCTACACGCCATAGAAAAGAAGTTGGACCTGCTTCAGTGCACTAACTAAGAAAAAGTCT

Reverse complement sequence

AGACTTTTTCTTAGTTAGTGCACTGAAGCAGGTCCAACTTCTTTTCTATGGCGTGTAGCCAATCACCAGCCTCAACTGGATTGGTAGTACTGGAAAAAGT[A/G]
GGCGGCCTCACACGAAGAAATTCTGCTAACTTGTTCTGGGGAGGAGCATGATTGTTCCCCTGGTTTTGTTGGTTCTGGAGTTGTTGCATCATCATGTTCA

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 75.30% 24.40% 0.21% 0.02% NA
All Indica  2759 95.50% 4.10% 0.33% 0.00% NA
All Japonica  1512 36.20% 63.70% 0.00% 0.07% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 87.40% 11.60% 1.01% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 95.40% 4.20% 0.38% 0.00% NA
Temperate Japonica  767 2.90% 97.10% 0.00% 0.00% NA
Tropical Japonica  504 81.00% 19.00% 0.00% 0.00% NA
Japonica Intermediate  241 49.00% 50.60% 0.00% 0.41% NA
VI/Aromatic  96 49.00% 50.00% 1.04% 0.00% NA
Intermediate  90 70.00% 30.00% 0.00% 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
vg0902272767 T -> DEL N N silent_mutation Average:31.247; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 N N N N
vg0902272767 T -> C LOC_Os09g04280.1 downstream_gene_variant ; 3222.0bp to feature; MODIFIER silent_mutation Average:31.247; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 N N N N
vg0902272767 T -> C LOC_Os09g04270.1 intron_variant ; MODIFIER silent_mutation Average:31.247; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0902272767 4.02E-06 NA mr1242 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
vg0902272767 NA 1.52E-09 mr1277 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
vg0902272767 NA 3.50E-08 mr1439 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
vg0902272767 7.31E-06 7.31E-06 mr1537 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
vg0902272767 1.92E-06 1.92E-06 mr1590 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
vg0902272767 NA 2.73E-07 mr1606 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
vg0902272767 NA 2.35E-08 mr1657 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
vg0902272767 NA 1.39E-06 mr1964 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
vg0902272767 NA 1.53E-14 mr1277_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
vg0902272767 NA 5.22E-07 mr1277_2 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
vg0902272767 NA 2.84E-06 mr1363_2 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
vg0902272767 NA 5.79E-06 mr1663_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
vg0902272767 NA 6.57E-06 mr1840_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