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Detailed information for vg0526439140:

Variant ID: vg0526439140 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 26439140
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGGATTGAGGCTGCTGGGGGTGACGACAGGGTCATGGCGAATTTCTTCCCCATGGTCCTAAAAGGTCAGGCGTGGGGTTGGCTGATGAACTTGTCACCC[G/A,T]
CGTCGGTACACTCTTGGGAGGATTTGTGCCAGCAGTTCACCATGAACTTCCAGGGCACATATCCGCGCCCAGGTGAAGAAGCGGACTTGCACGCGGTACA

Reverse complement sequence

TGTACCGCGTGCAAGTCCGCTTCTTCACCTGGGCGCGGATATGTGCCCTGGAAGTTCATGGTGAACTGCTGGCACAAATCCTCCCAAGAGTGTACCGACG[C/T,A]
GGGTGACAAGTTCATCAGCCAACCCCACGCCTGACCTTTTAGGACCATGGGGAAGAAATTCGCCATGACCCTGTCGTCACCCCCAGCAGCCTCAATCCCG

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 53.80% 5.40% 36.63% 4.08% T: 0.04%
All Indica  2759 27.30% 9.10% 56.83% 6.78% NA
All Japonica  1512 94.40% 0.10% 5.29% 0.20% NA
Aus  269 84.80% 0.40% 14.87% 0.00% NA
Indica I  595 4.90% 10.80% 77.14% 7.23% NA
Indica II  465 40.40% 6.50% 47.53% 5.59% NA
Indica III  913 33.20% 9.40% 50.60% 6.79% NA
Indica Intermediate  786 29.50% 9.20% 54.20% 7.12% NA
Temperate Japonica  767 97.30% 0.10% 2.22% 0.39% NA
Tropical Japonica  504 95.80% 0.20% 3.97% 0.00% NA
Japonica Intermediate  241 82.20% 0.00% 17.84% 0.00% NA
VI/Aromatic  96 76.00% 0.00% 20.83% 1.04% T: 2.08%
Intermediate  90 71.10% 1.10% 25.56% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0526439140 G -> T LOC_Os05g45620.1 missense_variant ; p.Ala294Ser; MODERATE nonsynonymous_codon ; A294S Average:33.894; most accessible tissue: Minghui63 flag leaf, score: 76.453 unknown unknown DELETERIOUS 0.00
vg0526439140 G -> DEL LOC_Os05g45620.1 N frameshift_variant Average:33.894; most accessible tissue: Minghui63 flag leaf, score: 76.453 N N N N
vg0526439140 G -> A LOC_Os05g45620.1 missense_variant ; p.Ala294Thr; MODERATE nonsynonymous_codon ; A294T Average:33.894; most accessible tissue: Minghui63 flag leaf, score: 76.453 unknown unknown DELETERIOUS 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0526439140 NA 2.79E-09 mr1193_2 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
vg0526439140 NA 4.84E-12 mr1349_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
vg0526439140 NA 6.71E-07 mr1896_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
vg0526439140 NA 7.52E-11 mr1907_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
vg0526439140 NA 2.24E-08 mr1934_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