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Detailed information for vg0818600655:

Variant ID: vg0818600655 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 18600655
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:


CCTCAACTTTGGAAGGCATTCCCTCCTTATTGGATTGAGCAAAAGTGGTGGGATATGTTGTGTGACTTGTGGTCTGATGAAAATGTAAAGAAAGTGTCAG[C/T]
TCAAAACAGCAAAAATCGGATGGAAGGAGGTGGTGTTCATCATACTTGTGGTTCACGAAGTGTTGCTATGCATAAACAAGCCATGGTACCAAAGTTAAAT

Reverse complement sequence

ATTTAACTTTGGTACCATGGCTTGTTTATGCATAGCAACACTTCGTGAACCACAAGTATGATGAACACCACCTCCTTCCATCCGATTTTTGCTGTTTTGA[G/A]
CTGACACTTTCTTTACATTTTCATCAGACCACAAGTCACACAACATATCCCACCACTTTTGCTCAATCCAATAAGGAGGGAATGCCTTCCAAAGTTGAGG

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 95.40% 1.60% 2.37% 0.61% NA
All Indica  2759 98.20% 0.80% 1.01% 0.00% NA
All Japonica  1512 89.20% 3.30% 5.56% 1.92% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 99.10% 0.40% 0.43% 0.00% NA
Indica III  913 97.30% 1.10% 1.64% 0.00% NA
Indica Intermediate  786 97.50% 1.10% 1.40% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 70.40% 9.50% 15.28% 4.76% NA
Japonica Intermediate  241 94.20% 0.80% 2.90% 2.07% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0818600655 C -> T LOC_Os08g30260.1 missense_variant ; p.Ala284Val; MODERATE nonsynonymous_codon ; A284V Average:21.54; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 unknown unknown DELETERIOUS 0.04
vg0818600655 C -> DEL LOC_Os08g30260.1 N frameshift_variant Average:21.54; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0818600655 NA 1.70E-07 mr1830 Jap_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
vg0818600655 6.58E-06 5.15E-10 mr1047_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
vg0818600655 NA 1.71E-09 mr1642_2 Jap_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