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Detailed information for vg1117387081:

Variant ID: vg1117387081 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17387081
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


CGTTGGTGCCATGAGCAGTAGCCTTGCCCAAATCCAATGACCAACTGCACGGGACGCCGCAGCGGTACTTCCCCATTGCCTCCATGCTTGAAATCCCATG[G/A]
ATCAGCGGCTCTGATACCATATTTTTAGCAACCAAATCACCAAACAACAAGAATTTCACCACGAACAACTATCCAGTCAACAGTGCTGTTTTTGGAGGTG

Reverse complement sequence

CACCTCCAAAAACAGCACTGTTGACTGGATAGTTGTTCGTGGTGAAATTCTTGTTGTTTGGTGATTTGGTTGCTAAAAATATGGTATCAGAGCCGCTGAT[C/T]
CATGGGATTTCAAGCATGGAGGCAATGGGGAAGTACCGCTGCGGCGTCCCGTGCAGTTGGTCATTGGATTTGGGCAAGGCTACTGCTCATGGCACCAACG

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 77.70% 21.90% 0.19% 0.15% NA
All Indica  2759 77.90% 21.60% 0.25% 0.25% NA
All Japonica  1512 87.80% 12.20% 0.00% 0.00% NA
Aus  269 13.80% 85.50% 0.74% 0.00% NA
Indica I  595 77.60% 22.40% 0.00% 0.00% NA
Indica II  465 78.10% 20.90% 0.43% 0.65% NA
Indica III  913 80.90% 19.10% 0.00% 0.00% NA
Indica Intermediate  786 74.40% 24.40% 0.64% 0.51% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 68.30% 31.70% 0.00% 0.00% NA
Japonica Intermediate  241 92.10% 7.90% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg1117387081 G -> A LOC_Os11g29920.1 synonymous_variant ; p.Ile956Ile; LOW synonymous_codon Average:25.701; most accessible tissue: Zhenshan97 flower, score: 46.765 N N N N
vg1117387081 G -> DEL LOC_Os11g29920.1 N frameshift_variant Average:25.701; most accessible tissue: Zhenshan97 flower, score: 46.765 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117387081 2.39E-06 NA mr1017 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
vg1117387081 3.39E-07 NA mr1132_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
vg1117387081 5.60E-06 NA mr1390_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
vg1117387081 2.62E-06 NA mr1490_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