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Detailed information for vg1003626827:

Variant ID: vg1003626827 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3626827
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


TGATTGTCTTAAAAAGATAAAATAGCAATAAATGTAGTGCGAAGTTACGAGTACAACCACTAAAGTTTAGTTCAAGGAGCAATTACATTCTTACCCCTGA[T/G]
TTGGAATGCAATTGTGATTTTACGTTTATTTGTGATTTTAGCCTTGTTTTTTCAAACGAAACCTTCTGTTTGTTCCTGTTTTTGGATGACAGTTTGGTGA

Reverse complement sequence

TCACCAAACTGTCATCCAAAAACAGGAACAAACAGAAGGTTTCGTTTGAAAAAACAAGGCTAAAATCACAAATAAACGTAAAATCACAATTGCATTCCAA[A/C]
TCAGGGGTAAGAATGTAATTGCTCCTTGAACTAAACTTTAGTGGTTGTACTCGTAACTTCGCACTACATTTATTGCTATTTTATCTTTTTAAGACAATCA

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 54.70% 45.20% 0.06% 0.00% NA
All Indica  2759 55.70% 44.20% 0.07% 0.00% NA
All Japonica  1512 46.70% 53.30% 0.00% 0.00% NA
Aus  269 88.50% 11.20% 0.37% 0.00% NA
Indica I  595 62.40% 37.60% 0.00% 0.00% NA
Indica II  465 61.70% 38.30% 0.00% 0.00% NA
Indica III  913 45.10% 54.90% 0.00% 0.00% NA
Indica Intermediate  786 59.50% 40.20% 0.25% 0.00% NA
Temperate Japonica  767 13.00% 87.00% 0.00% 0.00% NA
Tropical Japonica  504 92.50% 7.50% 0.00% 0.00% NA
Japonica Intermediate  241 58.10% 41.90% 0.00% 0.00% NA
VI/Aromatic  96 56.20% 43.80% 0.00% 0.00% NA
Intermediate  90 54.40% 45.60% 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
vg1003626827 T -> G LOC_Os10g06960.1 upstream_gene_variant ; 1117.0bp to feature; MODIFIER silent_mutation Average:54.337; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg1003626827 T -> G LOC_Os10g06970.1 downstream_gene_variant ; 2571.0bp to feature; MODIFIER silent_mutation Average:54.337; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg1003626827 T -> G LOC_Os10g06950-LOC_Os10g06960 intergenic_region ; MODIFIER silent_mutation Average:54.337; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003626827 NA 1.95E-06 mr1668 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
vg1003626827 NA 3.14E-06 mr1194_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
vg1003626827 NA 4.06E-07 mr1263_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
vg1003626827 4.63E-06 NA mr1624_2 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
vg1003626827 NA 4.23E-06 mr1780_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