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Detailed information for vg0718862748:

Variant ID: vg0718862748 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 18862748
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


ACTGAGAAGAACTTCAACTCTGGTGTGGGGGAAAAGAGAGCAAGACTGAGTACTACCCACTGTACTCAGCAAGTCATACCGGAAGAAAAGGTATGATGCA[G/A,T]
GATATATCCAAGGGAGGCTAAAGGTTCTTTAGCATAAAGCTAGCATTTAAAAGCAGTAGTTGAAAGCAGTAAAAACTGTTGTAGTAATTAATCAATATAA

Reverse complement sequence

TTATATTGATTAATTACTACAACAGTTTTTACTGCTTTCAACTACTGCTTTTAAATGCTAGCTTTATGCTAAAGAACCTTTAGCCTCCCTTGGATATATC[C/T,A]
TGCATCATACCTTTTCTTCCGGTATGACTTGCTGAGTACAGTGGGTAGTACTCAGTCTTGCTCTCTTTTCCCCCACACCAGAGTTGAAGTTCTTCTCAGT

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 93.00% 6.50% 0.53% 0.00% T: 0.02%
All Indica  2759 98.20% 0.90% 0.87% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 23.00% 76.20% 0.37% 0.00% T: 0.37%
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 96.90% 0.70% 2.41% 0.00% NA
Indica Intermediate  786 97.50% 2.30% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 30.20% 69.80% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0718862748 G -> A LOC_Os07g31760.1 downstream_gene_variant ; 4957.0bp to feature; MODIFIER silent_mutation Average:60.282; most accessible tissue: Minghui63 young leaf, score: 73.49 N N N N
vg0718862748 G -> A LOC_Os07g31750-LOC_Os07g31760 intergenic_region ; MODIFIER silent_mutation Average:60.282; most accessible tissue: Minghui63 young leaf, score: 73.49 N N N N
vg0718862748 G -> T LOC_Os07g31760.1 downstream_gene_variant ; 4957.0bp to feature; MODIFIER silent_mutation Average:60.282; most accessible tissue: Minghui63 young leaf, score: 73.49 N N N N
vg0718862748 G -> T LOC_Os07g31750-LOC_Os07g31760 intergenic_region ; MODIFIER silent_mutation Average:60.282; most accessible tissue: Minghui63 young leaf, score: 73.49 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0718862748 NA 3.51E-06 mr1006 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
vg0718862748 NA 2.45E-06 mr1052 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
vg0718862748 NA 2.97E-08 mr1126 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
vg0718862748 NA 1.90E-13 mr1231 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
vg0718862748 NA 1.81E-06 mr1262 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
vg0718862748 NA 6.72E-08 mr1415 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
vg0718862748 NA 3.71E-16 mr1522 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
vg0718862748 NA 6.72E-08 mr1567 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
vg0718862748 NA 4.98E-07 mr1652 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
vg0718862748 NA 1.66E-06 mr1662 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
vg0718862748 NA 6.34E-07 mr1762 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
vg0718862748 NA 8.08E-08 mr1522_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
vg0718862748 NA 2.73E-07 mr1567_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
vg0718862748 NA 2.04E-06 mr1929_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