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Detailed information for vg0625068802:

Variant ID: vg0625068802 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 25068802
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTAATTACACAGTGTGCGTGTAAATTGCGAGATGAATCTTTTAAGCCTAATTGCACCATGATTTAACAATGTGGTGCTACAGTAAACATTTACTAATAA[C/T]
GAATTAATTAGGCTTAATAAATTTGTCTCGCAGTTTCCTAGCGAAATCTGTAATTTGTTTTGTTATTAGACTACGTTTAGTATTTCAAATGTGTGTCCGT

Reverse complement sequence

ACGGACACACATTTGAAATACTAAACGTAGTCTAATAACAAAACAAATTACAGATTTCGCTAGGAAACTGCGAGACAAATTTATTAAGCCTAATTAATTC[G/A]
TTATTAGTAAATGTTTACTGTAGCACCACATTGTTAAATCATGGTGCAATTAGGCTTAAAAGATTCATCTCGCAATTTACACGCACACTGTGTAATTAGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.00% 9.00% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 73.10% 26.90% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 51.80% 48.20% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 84.60% 15.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0625068802 C -> T LOC_Os06g41810.1 downstream_gene_variant ; 4740.0bp to feature; MODIFIER silent_mutation Average:27.447; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0625068802 C -> T LOC_Os06g41800.1 intron_variant ; MODIFIER silent_mutation Average:27.447; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0625068802 3.80E-06 2.05E-06 mr1879_2 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