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Detailed information for vg0921818323:

Variant ID: vg0921818323 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 21818323
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TAATCAATCAATTGTTGAGTTGCTTATGCGTGTTGAATCATAGGGACATACCAAAAAGGGTAGCATCTAAGCCTTTGTTAGGCAAGTACTCATATATTAG[C/T]
AGTTTTTCATCTCCCTCAACACAACAGCCAAGAAGGCGAACCAAATTTCTGTGTTGCAATTTCGCGATAAGAATAACTTCATTCCTGAATTCCTTTGTCC

Reverse complement sequence

GGACAAAGGAATTCAGGAATGAAGTTATTCTTATCGCGAAATTGCAACACAGAAATTTGGTTCGCCTTCTTGGCTGTTGTGTTGAGGGAGATGAAAAACT[G/A]
CTAATATATGAGTACTTGCCTAACAAAGGCTTAGATGCTACCCTTTTTGGTATGTCCCTATGATTCAACACGCATAAGCAACTCAACAATTGATTGATTA

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 98.70% 1.20% 0.06% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 98.30% 1.60% 0.13% 0.00% NA
Aus  269 88.50% 11.50% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 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 98.70% 1.00% 0.26% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 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 97.80% 2.20% 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
vg0921818323 C -> T LOC_Os09g37840.1 synonymous_variant ; p.Leu579Leu; LOW synonymous_codon Average:35.067; most accessible tissue: Callus, score: 66.1 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0921818323 3.53E-07 NA mr1055_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