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Detailed information for vg0728979771:

Variant ID: vg0728979771 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 28979771
Reference Allele: AAlternative Allele: G,C
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, A: 0.24, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


GTGCTCTCCTTATCTTAGTTTGATCTTTTATTTCGTTGGGTGTGTTTAATTCATTTGAACTACACTCAGTGTTTGGGTGTTACTTTTATAATAATTGGCT[A/G,C]
TAGCTCTGATGAGCAAAGGCCGGGATGTTTTATTCTATTATTGTAGCGCCCGTTCCGTCGTGGCGCCTAGCGGAAAAATTATCTCTTAAAAACCCTAATT

Reverse complement sequence

AATTAGGGTTTTTAAGAGATAATTTTTCCGCTAGGCGCCACGACGGAACGGGCGCTACAATAATAGAATAAAACATCCCGGCCTTTGCTCATCAGAGCTA[T/C,G]
AGCCAATTATTATAAAAGTAACACCCAAACACTGAGTGTAGTTCAAATGAATTAAACACACCCAACGAAATAAAAGATCAAACTAAGATAAGGAGAGCAC

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 64.30% 28.50% 7.17% 0.00% C: 0.02%
All Indica  2759 82.30% 6.70% 10.91% 0.00% NA
All Japonica  1512 30.90% 67.30% 1.85% 0.00% NA
Aus  269 81.40% 17.10% 1.49% 0.00% NA
Indica I  595 88.10% 3.00% 8.91% 0.00% NA
Indica II  465 83.20% 6.50% 10.32% 0.00% NA
Indica III  913 79.70% 8.80% 11.50% 0.00% NA
Indica Intermediate  786 80.50% 7.40% 12.09% 0.00% NA
Temperate Japonica  767 1.30% 98.40% 0.26% 0.00% NA
Tropical Japonica  504 74.40% 21.00% 4.56% 0.00% NA
Japonica Intermediate  241 34.00% 64.70% 1.24% 0.00% NA
VI/Aromatic  96 30.20% 67.70% 2.08% 0.00% NA
Intermediate  90 56.70% 37.80% 4.44% 0.00% C: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0728979771 A -> G LOC_Os07g48440-LOC_Os07g48450 intergenic_region ; MODIFIER silent_mutation Average:11.542; most accessible tissue: Zhenshan97 flower, score: 16.6 N N N N
vg0728979771 A -> C LOC_Os07g48440-LOC_Os07g48450 intergenic_region ; MODIFIER silent_mutation Average:11.542; most accessible tissue: Zhenshan97 flower, score: 16.6 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0728979771 NA 2.99E-09 mr1304_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
vg0728979771 NA 3.71E-08 mr1308_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
vg0728979771 NA 1.70E-10 mr1347_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
vg0728979771 NA 3.56E-11 mr1368_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
vg0728979771 NA 4.15E-07 mr1401_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
vg0728979771 NA 4.17E-08 mr1551_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
vg0728979771 NA 1.36E-11 mr1552_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
vg0728979771 NA 4.53E-10 mr1584_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
vg0728979771 NA 5.84E-06 mr1606_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
vg0728979771 NA 6.64E-06 mr1866_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
vg0728979771 NA 9.62E-07 mr1905_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
vg0728979771 NA 5.93E-10 mr1916_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