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Detailed information for vg0807428797:

Variant ID: vg0807428797 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7428797
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.07, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


CGCGACCGACGCGAACCTGATTTCCAGATTAAGCCCTTCGCACATTTCTCTGAACTTGTTAGAGTCGAACTGCTTGCCGTTGTCAGTGATGAACTCTTTT[G/A]
GCACTCCGAAACGGCAAATAATGTTTTTCCATACAAACTTCTGTACTGCTGCCGAAGTGAATGCTCCGAGGGGTTCGGCCTCAATCCATCGGGAGAAGTA

Reverse complement sequence

TACTTCTCCCGATGGATTGAGGCCGAACCCCTCGGAGCATTCACTTCGGCAGCAGTACAGAAGTTTGTATGGAAAAACATTATTTGCCGTTTCGGAGTGC[C/T]
AAAAGAGTTCATCACTGACAACGGCAAGCAGTTCGACTCTAACAAGTTCAGAGAAATGTGCGAAGGGCTTAATCTGGAAATCAGGTTCGCGTCGGTCGCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.40% 43.90% 0.25% 0.51% NA
All Indica  2759 28.80% 70.00% 0.29% 0.87% NA
All Japonica  1512 97.90% 1.80% 0.26% 0.00% NA
Aus  269 77.00% 23.00% 0.00% 0.00% NA
Indica I  595 15.30% 81.70% 0.34% 2.69% NA
Indica II  465 49.50% 49.70% 0.00% 0.86% NA
Indica III  913 22.70% 76.80% 0.33% 0.22% NA
Indica Intermediate  786 34.00% 65.40% 0.38% 0.25% NA
Temperate Japonica  767 96.90% 2.60% 0.52% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 77.10% 22.90% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 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
vg0807428797 G -> A LOC_Os08g12550.1 missense_variant ; p.Pro295Leu; MODERATE nonsynonymous_codon ; P295L Average:43.929; most accessible tissue: Minghui63 young leaf, score: 75.937 benign 0.945 TOLERATED 0.07
vg0807428797 G -> DEL LOC_Os08g12550.1 N frameshift_variant Average:43.929; most accessible tissue: Minghui63 young leaf, score: 75.937 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807428797 NA 6.04E-06 mr1577 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