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Detailed information for vg0727553260:

Variant ID: vg0727553260 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27553260
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, A: 0.03, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TCCATATTTGTGCACTTTTAGATGATCCTAGTTTTCAAGTATATAGAACTGAGCGAGTACTGTAAGATTTGTAGATTCATCTTCTTCGGGGCCCTTGTTA[A/T]
GACTATACCTAAGTAATTGAGCTCCCTCAACTCACTCTAACATTGTGCTTTCAGGTTATTATCAGCATAGTTGGTCTTCTTTTATTTGGGAAATTATTAG

Reverse complement sequence

CTAATAATTTCCCAAATAAAAGAAGACCAACTATGCTGATAATAACCTGAAAGCACAATGTTAGAGTGAGTTGAGGGAGCTCAATTACTTAGGTATAGTC[T/A]
TAACAAGGGCCCCGAAGAAGATGAATCTACAAATCTTACAGTACTCGCTCAGTTCTATATACTTGAAAACTAGGATCATCTAAAAGTGCACAAATATGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.70% 14.30% 0.00% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 58.50% 41.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.60% 2.40% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 34.80% 65.20% 0.00% 0.00% NA
Tropical Japonica  504 88.30% 11.70% 0.00% 0.00% NA
Japonica Intermediate  241 71.80% 28.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg0727553260 A -> T LOC_Os07g46180.1 upstream_gene_variant ; 2613.0bp to feature; MODIFIER silent_mutation Average:52.329; most accessible tissue: Callus, score: 71.282 N N N N
vg0727553260 A -> T LOC_Os07g46160.1 downstream_gene_variant ; 2697.0bp to feature; MODIFIER silent_mutation Average:52.329; most accessible tissue: Callus, score: 71.282 N N N N
vg0727553260 A -> T LOC_Os07g46170.1 intron_variant ; MODIFIER silent_mutation Average:52.329; most accessible tissue: Callus, score: 71.282 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0727553260 3.36E-07 5.61E-12 mr1002 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
vg0727553260 NA 2.31E-13 mr1002 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
vg0727553260 8.90E-07 5.10E-15 mr1002_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
vg0727553260 NA 2.67E-14 mr1002_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
vg0727553260 NA 1.42E-09 mr1011_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
vg0727553260 NA 5.77E-07 mr1330_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
vg0727553260 NA 1.66E-08 mr1454_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