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Detailed information for vg0432427836:

Variant ID: vg0432427836 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32427836
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.84, C: 0.15, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


TAAAGATCGATCTTTAGTCCCGGTTGGTAATACCAACCGGGACTAAAGATGTAGCGCCCGTTCCGTCGTGGCGCCTAGCGGGAAAATTATCTCCTAAAAA[T/C]
CCTAATTGCGAAATTTGTTTCTTTGCTTGTTGTCTAGTGTCCGTGCCATCTCAAGATCTCAATCCCCGATCTATCGTCGAGTTCAATTCCGAATCCAAAT

Reverse complement sequence

ATTTGGATTCGGAATTGAACTCGACGATAGATCGGGGATTGAGATCTTGAGATGGCACGGACACTAGACAACAAGCAAAGAAACAAATTTCGCAATTAGG[A/G]
TTTTTAGGAGATAATTTTCCCGCTAGGCGCCACGACGGAACGGGCGCTACATCTTTAGTCCCGGTTGGTATTACCAACCGGGACTAAAGATCGATCTTTA

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 69.60% 3.20% 5.16% 22.05% NA
All Indica  2759 71.30% 0.20% 3.33% 25.19% NA
All Japonica  1512 77.70% 9.30% 7.54% 5.42% NA
Aus  269 20.10% 1.10% 1.49% 77.32% NA
Indica I  595 91.90% 0.00% 0.17% 7.90% NA
Indica II  465 73.80% 0.60% 2.37% 23.23% NA
Indica III  913 50.80% 0.00% 7.89% 41.29% NA
Indica Intermediate  786 78.00% 0.30% 1.02% 20.74% NA
Temperate Japonica  767 78.10% 12.90% 8.74% 0.26% NA
Tropical Japonica  504 75.60% 2.00% 7.34% 15.08% NA
Japonica Intermediate  241 80.90% 13.30% 4.15% 1.66% NA
VI/Aromatic  96 25.00% 0.00% 32.29% 42.71% NA
Intermediate  90 74.40% 4.40% 3.33% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0432427836 T -> C LOC_Os04g54510.1 upstream_gene_variant ; 2218.0bp to feature; MODIFIER silent_mutation Average:42.145; most accessible tissue: Zhenshan97 flower, score: 63.345 N N N N
vg0432427836 T -> C LOC_Os04g54500.1 downstream_gene_variant ; 3839.0bp to feature; MODIFIER silent_mutation Average:42.145; most accessible tissue: Zhenshan97 flower, score: 63.345 N N N N
vg0432427836 T -> C LOC_Os04g54520.1 downstream_gene_variant ; 2193.0bp to feature; MODIFIER silent_mutation Average:42.145; most accessible tissue: Zhenshan97 flower, score: 63.345 N N N N
vg0432427836 T -> C LOC_Os04g54510-LOC_Os04g54520 intergenic_region ; MODIFIER silent_mutation Average:42.145; most accessible tissue: Zhenshan97 flower, score: 63.345 N N N N
vg0432427836 T -> DEL N N silent_mutation Average:42.145; most accessible tissue: Zhenshan97 flower, score: 63.345 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432427836 6.33E-10 1.03E-12 Grain_weight All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652