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Detailed information for vg1021824431:

Variant ID: vg1021824431 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 21824431
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GAACCGGGGTCAATACTGCCTAAGCACCTATAATGATCCGGTTATATAAGTTTAGGGATGCCATATATCTGATTTTCGGTTCAAAGACGATTTTTTAACT[T/C]
CGTGACAAGATGGGAGATCTTAGGTGAACTTTTTTCCTTTGCGAATACATCAATGTTTGCTAGCCTCTCCTCCCTATTGTGTTGGTTCATTTTGCAATGG

Reverse complement sequence

CCATTGCAAAATGAACCAACACAATAGGGAGGAGAGGCTAGCAAACATTGATGTATTCGCAAAGGAAAAAAGTTCACCTAAGATCTCCCATCTTGTCACG[A/G]
AGTTAAAAAATCGTCTTTGAACCGAAAATCAGATATATGGCATCCCTAAACTTATATAACCGGATCATTATAGGTGCTTAGGCAGTATTGACCCCGGTTC

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 89.40% 9.60% 1.04% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 68.10% 28.70% 3.17% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 45.80% 49.50% 4.69% 0.00% NA
Tropical Japonica  504 95.20% 4.40% 0.40% 0.00% NA
Japonica Intermediate  241 82.60% 13.30% 4.15% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg1021824431 T -> C LOC_Os10g40680.1 downstream_gene_variant ; 731.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021824431 T -> C LOC_Os10g40680-LOC_Os10g40700 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1021824431 NA 3.65E-07 mr1162 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
vg1021824431 NA 3.21E-06 mr1164 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
vg1021824431 2.60E-06 NA mr1518 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
vg1021824431 NA 5.71E-08 mr1617 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
vg1021824431 NA 6.88E-07 mr1748 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
vg1021824431 NA 6.64E-06 mr1786 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
vg1021824431 NA 2.81E-06 mr1955 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