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Detailed information for vg0718910920:

Variant ID: vg0718910920 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 18910920
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


CGTCATTTATTTTTTCTCACATGTTTGACCATTCGTCTTATTTAAAAAATTTACGTAATTATAATTTATTTTGTTATGAGTTGTTTTATCACTCATAGTA[C/T]
TTTAAGTGTGATTTATATCTTATACATTTGCATAAAATTTTGAATAAGACGAATGATCAAACATGTGAGAAAAAGTCAACGGCGTCATCTATTAAAAAAC

Reverse complement sequence

GTTTTTTAATAGATGACGCCGTTGACTTTTTCTCACATGTTTGATCATTCGTCTTATTCAAAATTTTATGCAAATGTATAAGATATAAATCACACTTAAA[G/A]
TACTATGAGTGATAAAACAACTCATAACAAAATAAATTATAATTACGTAAATTTTTTAAATAAGACGAATGGTCAAACATGTGAGAAAAAATAAATGACG

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 77.00% 22.90% 0.11% 0.00% NA
All Indica  2759 61.80% 38.00% 0.14% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 92.60% 7.10% 0.37% 0.00% NA
Indica I  595 21.20% 78.30% 0.50% 0.00% NA
Indica II  465 68.00% 32.00% 0.00% 0.00% NA
Indica III  913 85.00% 15.00% 0.00% 0.00% NA
Indica Intermediate  786 62.10% 37.80% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0718910920 C -> T LOC_Os07g31810.1 upstream_gene_variant ; 4150.0bp to feature; MODIFIER silent_mutation Average:38.416; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0718910920 C -> T LOC_Os07g31830.1 upstream_gene_variant ; 867.0bp to feature; MODIFIER silent_mutation Average:38.416; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0718910920 C -> T LOC_Os07g31840.1 downstream_gene_variant ; 4024.0bp to feature; MODIFIER silent_mutation Average:38.416; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0718910920 C -> T LOC_Os07g31810-LOC_Os07g31830 intergenic_region ; MODIFIER silent_mutation Average:38.416; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0718910920 9.26E-07 1.15E-06 mr1480 Ind_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
vg0718910920 6.49E-07 3.82E-06 mr1692 Ind_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
vg0718910920 NA 1.63E-06 mr1125_2 Ind_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
vg0718910920 NA 1.40E-06 mr1910_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