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Detailed information for vg0818600407:

Variant ID: vg0818600407 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 18600407
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGGTTCTTTTAATGGATTGACGTCCTACCTTATCCTTTTACAGCTGCGTTTTAAGTTTGCTGATGGTAGAGAAGTGGATTGTGCTAGATTATTTTATCG[C/T]
AAAGCTGTTGAACGTTTTAGCCAAGCTTTGTCACATGAGAAATCTGAAGCAAAACGTTCTTTGGAAAAGCATATCGAAAATATGCGTGCGACTGAGTTAC

Reverse complement sequence

GTAACTCAGTCGCACGCATATTTTCGATATGCTTTTCCAAAGAACGTTTTGCTTCAGATTTCTCATGTGACAAAGCTTGGCTAAAACGTTCAACAGCTTT[G/A]
CGATAAAATAATCTAGCACAATCCACTTCTCTACCATCAGCAAACTTAAAACGCAGCTGTAAAAGGATAAGGTAGGACGTCAATCCATTAAAAGAACCTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.80% 3.70% 0.74% 0.68% NA
All Indica  2759 98.50% 1.00% 0.54% 0.00% NA
All Japonica  1512 87.00% 9.70% 1.19% 2.12% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.90% 0.90% 0.22% 0.00% NA
Indica III  913 97.80% 1.30% 0.88% 0.00% NA
Indica Intermediate  786 98.00% 1.30% 0.76% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 65.30% 26.80% 2.78% 5.16% NA
Japonica Intermediate  241 91.30% 4.60% 1.66% 2.49% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 4.40% 2.22% 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
vg0818600407 C -> T LOC_Os08g30260.1 synonymous_variant ; p.Arg201Arg; LOW synonymous_codon Average:22.116; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0818600407 C -> DEL LOC_Os08g30260.1 N frameshift_variant Average:22.116; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0818600407 NA 1.02E-06 mr1073 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
vg0818600407 2.89E-08 2.89E-08 mr1266 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
vg0818600407 NA 1.33E-06 mr1345 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
vg0818600407 NA 2.47E-06 mr1638 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
vg0818600407 1.02E-06 5.83E-10 mr1830 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
vg0818600407 NA 7.43E-07 mr1852 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
vg0818600407 NA 1.69E-06 mr1866 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
vg0818600407 NA 2.50E-08 mr1047_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