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Detailed information for vg1125530448:

Variant ID: vg1125530448 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25530448
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGTGTATAATTTCTGACAGTTGCAAAGATGAATACTTTTATCATAGCTCTGATGCCTATTCTTTGGTATCTGGGCAATGCCATCCAATATTCAGGTCC[G/A]
CTGGGACAGGAAAGCTTCGGATGGTGGAGGATAGACTTATGCAGCAAAAAGCGCAATTGTTACTGGATGAGGCTGCTTCTTGGTCACTTCTTTGGTACCT

Reverse complement sequence

AGGTACCAAAGAAGTGACCAAGAAGCAGCCTCATCCAGTAACAATTGCGCTTTTTGCTGCATAAGTCTATCCTCCACCATCCGAAGCTTTCCTGTCCCAG[C/T]
GGACCTGAATATTGGATGGCATTGCCCAGATACCAAAGAATAGGCATCAGAGCTATGATAAAAGTATTCATCTTTGCAACTGTCAGAAATTATACACAAA

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 90.30% 9.70% 0.00% 0.00% NA
All Indica  2759 92.60% 7.40% 0.00% 0.00% NA
All Japonica  1512 88.40% 11.60% 0.00% 0.00% NA
Aus  269 73.20% 26.80% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 83.40% 16.60% 0.00% 0.00% NA
Indica Intermediate  786 96.80% 3.20% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 71.80% 28.20% 0.00% 0.00% NA
Japonica Intermediate  241 89.60% 10.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg1125530448 G -> A LOC_Os11g42420.1 missense_variant ; p.Ala177Thr; MODERATE nonsynonymous_codon ; A177T Average:46.318; most accessible tissue: Callus, score: 62.534 benign 1.442 DELETERIOUS 0.01
vg1125530448 G -> A LOC_Os11g42420.2 missense_variant ; p.Ala177Thr; MODERATE nonsynonymous_codon ; A177T Average:46.318; most accessible tissue: Callus, score: 62.534 benign 1.442 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125530448 3.56E-06 NA mr1238 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
vg1125530448 NA 7.68E-07 mr1543 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
vg1125530448 2.23E-07 9.47E-07 mr1662 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
vg1125530448 5.22E-06 7.21E-07 mr1662 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
vg1125530448 3.34E-06 7.94E-09 mr1662_2 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
vg1125530448 8.41E-06 7.07E-06 mr1662_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