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Detailed information for vg1005694637:

Variant ID: vg1005694637 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5694637
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.76, G: 0.23, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGCTGAGGCATGCAAATCAAGCGAAGCTCTACCAAATCATCCAGCTGGTGAAGTACATTTGAGATGCTCCTCAGCATGGTACACTTGAGAGTCAAAAC[A/G]
GCGAGAAACGCCATGGATCCCTGCTGCAAATTCCACTCCTCCAAACCAATATCCATAAGTACCAAACTGCGTAATGCAAGGAATCCCTCGGAAGAACATG

Reverse complement sequence

CATGTTCTTCCGAGGGATTCCTTGCATTACGCAGTTTGGTACTTATGGATATTGGTTTGGAGGAGTGGAATTTGCAGCAGGGATCCATGGCGTTTCTCGC[T/C]
GTTTTGACTCTCAAGTGTACCATGCTGAGGAGCATCTCAAATGTACTTCACCAGCTGGATGATTTGGTAGAGCTTCGCTTGATTTGCATGCCTCAGCTCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.70% 4.30% 0.08% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 92.70% 7.10% 0.20% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
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 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 87.50% 12.10% 0.39% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 35.40% 64.60% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 1.11% 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
vg1005694637 A -> G LOC_Os10g10360.1 synonymous_variant ; p.Ala834Ala; LOW synonymous_codon Average:56.479; most accessible tissue: Zhenshan97 young leaf, score: 81.353 N N N N
vg1005694637 A -> G LOC_Os10g10360.4 synonymous_variant ; p.Ala801Ala; LOW synonymous_codon Average:56.479; most accessible tissue: Zhenshan97 young leaf, score: 81.353 N N N N
vg1005694637 A -> G LOC_Os10g10360.3 synonymous_variant ; p.Ala834Ala; LOW synonymous_codon Average:56.479; most accessible tissue: Zhenshan97 young leaf, score: 81.353 N N N N
vg1005694637 A -> G LOC_Os10g10360.2 synonymous_variant ; p.Ala834Ala; LOW synonymous_codon Average:56.479; most accessible tissue: Zhenshan97 young leaf, score: 81.353 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005694637 8.09E-12 NA mr1210 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
vg1005694637 4.54E-06 1.56E-09 mr1210 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
vg1005694637 NA 5.67E-06 mr1300 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
vg1005694637 2.38E-12 NA mr1305 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
vg1005694637 2.95E-06 1.84E-09 mr1305 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
vg1005694637 2.68E-07 1.50E-12 mr1585 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
vg1005694637 1.80E-06 7.09E-12 mr1585 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
vg1005694637 5.44E-12 NA mr1586 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
vg1005694637 NA 1.09E-08 mr1586 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
vg1005694637 8.82E-06 NA mr1649 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
vg1005694637 2.00E-09 NA mr1305_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
vg1005694637 5.16E-07 8.16E-10 mr1305_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
vg1005694637 1.48E-08 9.69E-14 mr1585_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
vg1005694637 6.77E-08 4.10E-13 mr1585_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