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Detailed information for vg0723902655:

Variant ID: vg0723902655 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 23902655
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGATGCGGTTTCTCGGCGTGTTTTTTTTTTCTTTTTGTTCTGTTCAACCTGACGCTAGCAGAAGTTCAGAACTAGGAACTCGCCGTGGCAGACTTAGGG[C/T]
CTATTCACTTTAATGCCAAAAAAAACCTTACCAAATTTTAGCAACTTGCTAAAAATTTTGCAGGATTTCTTATATAGTTACCAAAATTTGGCAAGAAATT

Reverse complement sequence

AATTTCTTGCCAAATTTTGGTAACTATATAAGAAATCCTGCAAAATTTTTAGCAAGTTGCTAAAATTTGGTAAGGTTTTTTTTGGCATTAAAGTGAATAG[G/A]
CCCTAAGTCTGCCACGGCGAGTTCCTAGTTCTGAACTTCTGCTAGCGTCAGGTTGAACAGAACAAAAAGAAAAAAAAAACACGCCGAGAAACCGCATCCA

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 96.50% 2.90% 0.57% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 89.60% 8.60% 1.79% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 92.80% 4.30% 2.87% 0.00% NA
Tropical Japonica  504 91.50% 8.30% 0.20% 0.00% NA
Japonica Intermediate  241 75.50% 22.80% 1.66% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0723902655 C -> T LOC_Os07g39850.1 upstream_gene_variant ; 3013.0bp to feature; MODIFIER silent_mutation Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0723902655 C -> T LOC_Os07g39860.1 downstream_gene_variant ; 219.0bp to feature; MODIFIER silent_mutation Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0723902655 C -> T LOC_Os07g39870.1 downstream_gene_variant ; 2265.0bp to feature; MODIFIER silent_mutation Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0723902655 C -> T LOC_Os07g39870.2 downstream_gene_variant ; 2265.0bp to feature; MODIFIER silent_mutation Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0723902655 C -> T LOC_Os07g39870.3 downstream_gene_variant ; 2265.0bp to feature; MODIFIER silent_mutation Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0723902655 C -> T LOC_Os07g39850-LOC_Os07g39860 intergenic_region ; MODIFIER silent_mutation Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0723902655 1.77E-06 1.98E-08 mr1350_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