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Detailed information for vg0214439802:

Variant ID: vg0214439802 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 14439802
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:


TAAGAAATACCAACATTCACCAAGGCAGGGGATGAGGTGCTCCACAAGTATGTCACACCCACCGCTACTCCATCCACTCCAAAGGAGGAGCGGTTTTGCA[T/A]
TATGGGAGTGCGAACTCCCAGCGGTGGGTATGGCAAGGGTTTGCTCCGGCCTTTGACAGCAACGGAGAAGGAGGGGGCAGCAGAATCTCGTATCCCTCCA

Reverse complement sequence

TGGAGGGATACGAGATTCTGCTGCCCCCTCCTTCTCCGTTGCTGTCAAAGGCCGGAGCAAACCCTTGCCATACCCACCGCTGGGAGTTCGCACTCCCATA[A/T]
TGCAAAACCGCTCCTCCTTTGGAGTGGATGGAGTAGCGGTGGGTGTGACATACTTGTGGAGCACCTCATCCCCTGCCTTGGTGAATGTTGGTATTTCTTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.50% 1.50% 2.84% 12.12% NA
All Indica  2759 72.40% 2.40% 4.82% 20.41% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 95.90% 0.70% 0.37% 2.97% NA
Indica I  595 69.70% 3.40% 5.38% 21.51% NA
Indica II  465 83.00% 0.90% 3.87% 12.26% NA
Indica III  913 67.40% 2.10% 4.93% 25.63% NA
Indica Intermediate  786 73.90% 2.90% 4.83% 18.32% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0214439802 T -> A LOC_Os02g24910.1 missense_variant ; p.Ile57Asn; MODERATE nonsynonymous_codon ; I57N Average:41.997; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 probably damaging 2.422 DELETERIOUS 0.04
vg0214439802 T -> DEL LOC_Os02g24910.1 N frameshift_variant Average:41.997; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0214439802 8.90E-07 9.43E-06 mr1242 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