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Detailed information for vg0315011365:

Variant ID: vg0315011365 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15011365
Reference Allele: CAlternative Allele: T,G
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGACAGGCTGATGTGGCTGCAGGCCTTCCTCCGGGAGGCCGACGCCAAGCGACGCGCCGTCTCCGACGAGGTCAACAAGGTGTGGCTGCTGCAGACGCG[C/T,G]
GACGCCGTCTTCGACGCCGAGGACGCCCTCGATCATTTCTATCTCCGCGTCGATATGTCCAGGTATATATAGCTGCTACTAGATACTCCCTCTATTTTTT

Reverse complement sequence

AAAAAATAGAGGGAGTATCTAGTAGCAGCTATATATACCTGGACATATCGACGCGGAGATAGAAATGATCGAGGGCGTCCTCGGCGTCGAAGACGGCGTC[G/A,C]
CGCGTCTGCAGCAGCCACACCTTGTTGACCTCGTCGGAGACGGCGCGTCGCTTGGCGTCGGCCTCCCGGAGGAAGGCCTGCAGCCACATCAGCCTGTCCC

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 79.20% 20.80% 0.02% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 40.30% 59.70% 0.07% 0.00% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 11.50% 88.40% 0.13% 0.00% NA
Tropical Japonica  504 74.60% 25.40% 0.00% 0.00% NA
Japonica Intermediate  241 60.20% 39.80% 0.00% 0.00% NA
VI/Aromatic  96 45.80% 54.20% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0315011365 C -> T LOC_Os03g26250.1 synonymous_variant ; p.Arg68Arg; LOW synonymous_codon Average:67.981; most accessible tissue: Minghui63 root, score: 82.967 N N N N
vg0315011365 C -> G LOC_Os03g26250.1 synonymous_variant ; p.Arg68Arg; LOW N Average:67.981; most accessible tissue: Minghui63 root, score: 82.967 N N N N
vg0315011365 C -> G LOC_Os03g26240.1 upstream_gene_variant ; 1912.0bp to feature; MODIFIER N Average:67.981; most accessible tissue: Minghui63 root, score: 82.967 N N N N
vg0315011365 C -> G LOC_Os03g26260.1 upstream_gene_variant ; 4441.0bp to feature; MODIFIER N Average:67.981; most accessible tissue: Minghui63 root, score: 82.967 N N N N
vg0315011365 C -> G LOC_Os03g26229.1 downstream_gene_variant ; 3105.0bp to feature; MODIFIER N Average:67.981; most accessible tissue: Minghui63 root, score: 82.967 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315011365 NA 4.89E-06 mr1448 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
vg0315011365 NA 1.01E-09 mr1549 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
vg0315011365 NA 1.80E-06 mr1627 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
vg0315011365 NA 3.26E-08 mr1757 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