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Detailed information for vg0810503248:

Variant ID: vg0810503248 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10503248
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAGGAACTGTGTTTAGGATCTGTGTGACTTGCCTTGCAATAATCGGTCTTCAATTAGTCTTCAGAACCACTTCCGACGCACTCGCGAACCTTTCGCAAC[G/A]
ACGGAAACAACAAGCTAACACGCAAAATGGGAAAAAAGACTAATAAAAACCAAATAAACAGTACATAAAAGTAAACAAACATGTAGATCATGATTTTAGA

Reverse complement sequence

TCTAAAATCATGATCTACATGTTTGTTTACTTTTATGTACTGTTTATTTGGTTTTTATTAGTCTTTTTTCCCATTTTGCGTGTTAGCTTGTTGTTTCCGT[C/T]
GTTGCGAAAGGTTCGCGAGTGCGTCGGAAGTGGTTCTGAAGACTAATTGAAGACCGATTATTGCAAGGCAAGTCACACAGATCCTAAACACAGTTCCTTT

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 95.30% 4.70% 0.02% 0.00% NA
All Indica  2759 98.50% 1.50% 0.04% 0.00% NA
All Japonica  1512 96.40% 3.60% 0.00% 0.00% NA
Aus  269 53.20% 46.80% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.80% 0.13% 0.00% NA
Temperate Japonica  767 93.20% 6.80% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0810503248 G -> A LOC_Os08g17150.1 upstream_gene_variant ; 491.0bp to feature; MODIFIER silent_mutation Average:40.659; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg0810503248 G -> A LOC_Os08g17160.1 upstream_gene_variant ; 4876.0bp to feature; MODIFIER silent_mutation Average:40.659; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg0810503248 G -> A LOC_Os08g17140-LOC_Os08g17150 intergenic_region ; MODIFIER silent_mutation Average:40.659; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810503248 NA 1.49E-06 mr1028 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
vg0810503248 NA 7.02E-06 mr1453 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
vg0810503248 NA 1.88E-06 mr1648 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
vg0810503248 NA 7.37E-06 mr1652 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
vg0810503248 NA 6.23E-07 mr1697 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
vg0810503248 8.12E-06 NA mr1757 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
vg0810503248 NA 5.54E-06 mr1458_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