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Detailed information for vg1117961302:

Variant ID: vg1117961302 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17961302
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, G: 0.30, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:


CGGGTAGGGCAAACATTTCTCCCACTCCTTGCTAAAATCCAATGCACAAGCTCTCAACATGTCCTCCAAGACCTGGTTTGTTCTCTCTGTCTGGCCATCC[G/A]
TTTGCGGGTGATAAGCTGTGCTAAAAGCAAGGTAACTTCCTAGGGCTTCATGTACTTTTTCCCAGAAATACGAGGTAAACTGTGTGCCTCGATCGGATAT

Reverse complement sequence

ATATCCGATCGAGGCACACAGTTTACCTCGTATTTCTGGGAAAAAGTACATGAAGCCCTAGGAAGTTACCTTGCTTTTAGCACAGCTTATCACCCGCAAA[C/T]
GGATGGCCAGACAGAGAGAACAAACCAGGTCTTGGAGGACATGTTGAGAGCTTGTGCATTGGATTTTAGCAAGGAGTGGGAGAAATGTTTGCCCTACCCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.20% 39.90% 0.91% 9.06% NA
All Indica  2759 79.40% 17.90% 1.16% 1.56% NA
All Japonica  1512 5.80% 71.60% 0.60% 21.96% NA
Aus  269 14.50% 84.80% 0.00% 0.74% NA
Indica I  595 71.80% 24.20% 2.69% 1.34% NA
Indica II  465 75.10% 24.30% 0.43% 0.22% NA
Indica III  913 85.50% 11.30% 0.66% 2.52% NA
Indica Intermediate  786 80.50% 17.00% 1.02% 1.40% NA
Temperate Japonica  767 1.40% 96.70% 0.13% 1.69% NA
Tropical Japonica  504 12.30% 47.80% 1.39% 38.49% NA
Japonica Intermediate  241 6.20% 41.50% 0.41% 51.87% NA
VI/Aromatic  96 8.30% 42.70% 1.04% 47.92% NA
Intermediate  90 51.10% 42.20% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117961302 G -> A LOC_Os11g30850.1 missense_variant ; p.Thr150Met; MODERATE nonsynonymous_codon ; T150M Average:57.678; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 unknown unknown DELETERIOUS 0.01
vg1117961302 G -> DEL LOC_Os11g30850.1 N frameshift_variant Average:57.678; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117961302 NA 5.58E-06 mr1094 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
vg1117961302 NA 2.70E-06 mr1096 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
vg1117961302 NA 2.38E-06 mr1121 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
vg1117961302 NA 1.22E-07 mr1068_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
vg1117961302 NA 9.36E-06 mr1078_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
vg1117961302 NA 2.73E-06 mr1091_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
vg1117961302 NA 9.59E-07 mr1094_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
vg1117961302 NA 3.40E-07 mr1096_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
vg1117961302 NA 2.74E-07 mr1110_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
vg1117961302 4.59E-06 4.59E-06 mr1111_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
vg1117961302 NA 3.61E-06 mr1112_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
vg1117961302 NA 4.39E-07 mr1121_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
vg1117961302 NA 8.63E-07 mr1211_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