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Detailed information for vg0910354924:

Variant ID: vg0910354924 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10354924
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


TATTGCCAATGATGTTGAGATCATCGACATATACCGAGATAATACAAAATCCTGTGGTGGACTTTTTGATAAAGACGCACGGGCAATCATCATTTTTAGT[G/A]
TATCCCTTTAGCGAAAGGAATTCACTCAATCGGTTGTACCACATCCTGCCCGATTGTTTTAAGCCATAAAGTGACTTCTGCAACTTAACACAATACATGT

Reverse complement sequence

ACATGTATTGTGTTAAGTTGCAGAAGTCACTTTATGGCTTAAAACAATCGGGCAGGATGTGGTACAACCGATTGAGTGAATTCCTTTCGCTAAAGGGATA[C/T]
ACTAAAAATGATGATTGCCCGTGCGTCTTTATCAAAAAGTCCACCACAGGATTTTGTATTATCTCGGTATATGTCGATGATCTCAACATCATTGGCAATA

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 92.10% 7.80% 0.13% 0.00% NA
All Indica  2759 87.60% 12.30% 0.18% 0.00% NA
All Japonica  1512 98.00% 1.90% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.10% 3.70% 0.17% 0.00% NA
Indica II  465 90.30% 9.70% 0.00% 0.00% NA
Indica III  913 79.70% 19.90% 0.33% 0.00% NA
Indica Intermediate  786 88.50% 11.30% 0.13% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 97.60% 2.20% 0.20% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg0910354924 G -> A LOC_Os09g16930.1 synonymous_variant ; p.Tyr727Tyr; LOW synonymous_codon Average:10.795; most accessible tissue: Zhenshan97 flower, score: 14.863 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0910354924 3.75E-06 5.55E-06 mr1120 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
vg0910354924 NA 6.81E-06 mr1247_2 Ind_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