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Detailed information for vg1223326459:

Variant ID: vg1223326459 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23326459
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCTATCCTGGACCACCTATTGAGGAGAACACCAAATATATCATCCATAGTAGTAGAGAAATTAAGCTCTTTGTTCTTGACATTATCCTTTGGATCATA[T/C]
CATACCTGTTTCCCCACCGAGCATGGAGCTCAAGGATGAGGCGCTCTTCATGCGGAGACATGCGCCCACGCTTGAGGCCAGGGTGGAGGTAGTTGACCCA

Reverse complement sequence

TGGGTCAACTACCTCCACCCTGGCCTCAAGCGTGGGCGCATGTCTCCGCATGAAGAGCGCCTCATCCTTGAGCTCCATGCTCGGTGGGGAAACAGGTATG[A/G]
TATGATCCAAAGGATAATGTCAAGAACAAAGAGCTTAATTTCTCTACTACTATGGATGATATATTTGGTGTTCTCCTCAATAGGTGGTCCAGGATAGCAA

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 95.50% 3.30% 1.25% 0.00% NA
All Indica  2759 92.30% 5.50% 2.14% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 68.60% 22.40% 9.08% 0.00% NA
Indica II  465 98.30% 1.10% 0.65% 0.00% NA
Indica III  913 99.80% 0.00% 0.22% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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 98.90% 1.10% 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
vg1223326459 T -> C LOC_Os12g37970.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:76.787; most accessible tissue: Zhenshan97 flower, score: 82.948 N N N N
vg1223326459 T -> C LOC_Os12g37970.2 splice_region_variant&intron_variant ; LOW silent_mutation Average:76.787; most accessible tissue: Zhenshan97 flower, score: 82.948 N N N N
vg1223326459 T -> C LOC_Os12g37970.3 splice_region_variant&intron_variant ; LOW silent_mutation Average:76.787; most accessible tissue: Zhenshan97 flower, score: 82.948 N N N N
vg1223326459 T -> C LOC_Os12g37960.1 downstream_gene_variant ; 2706.0bp to feature; MODIFIER silent_mutation Average:76.787; most accessible tissue: Zhenshan97 flower, score: 82.948 N N N N
vg1223326459 T -> C LOC_Os12g37960.2 downstream_gene_variant ; 2706.0bp to feature; MODIFIER silent_mutation Average:76.787; most accessible tissue: Zhenshan97 flower, score: 82.948 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223326459 NA 5.28E-08 mr1709_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