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Detailed information for vg0434560709:

Variant ID: vg0434560709 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34560709
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


CAGTCGGAATTATCCGGAAATTCTCGGATTCGGAAACGAATTCGGATATTTTTTCTTGGAAACGAAAACGAATACAGTAAGGGTAATATCCGTCGGAATC[A/G]
GAAAACGGTCGGAAACTATCCAGAATTTTTTTCAGATATCCGCAGACATTAAGCAAATTATATAAAAAACACGTATATATACATAACTTTTTCATACGGA

Reverse complement sequence

TCCGTATGAAAAAGTTATGTATATATACGTGTTTTTTATATAATTTGCTTAATGTCTGCGGATATCTGAAAAAAATTCTGGATAGTTTCCGACCGTTTTC[T/C]
GATTCCGACGGATATTACCCTTACTGTATTCGTTTTCGTTTCCAAGAAAAAATATCCGAATTCGTTTCCGAATCCGAGAATTTCCGGATAATTCCGACTG

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 70.10% 28.70% 1.23% 0.00% NA
All Indica  2759 97.50% 1.70% 0.76% 0.00% NA
All Japonica  1512 21.50% 76.50% 2.05% 0.00% NA
Aus  269 71.70% 27.90% 0.37% 0.00% NA
Indica I  595 98.00% 0.80% 1.18% 0.00% NA
Indica II  465 97.60% 1.10% 1.29% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 94.80% 4.20% 1.02% 0.00% NA
Temperate Japonica  767 19.00% 77.40% 3.52% 0.00% NA
Tropical Japonica  504 9.10% 90.50% 0.40% 0.00% NA
Japonica Intermediate  241 55.20% 44.00% 0.83% 0.00% NA
VI/Aromatic  96 58.30% 41.70% 0.00% 0.00% NA
Intermediate  90 52.20% 42.20% 5.56% 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
vg0434560709 A -> G LOC_Os04g58020.1 upstream_gene_variant ; 1150.0bp to feature; MODIFIER silent_mutation Average:32.024; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0434560709 A -> G LOC_Os04g58030.1 downstream_gene_variant ; 3675.0bp to feature; MODIFIER silent_mutation Average:32.024; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0434560709 A -> G LOC_Os04g58020-LOC_Os04g58030 intergenic_region ; MODIFIER silent_mutation Average:32.024; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434560709 NA 9.70E-09 mr1117 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
vg0434560709 NA 1.27E-11 mr1118 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
vg0434560709 NA 2.34E-08 mr1123 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
vg0434560709 NA 1.10E-06 mr1239 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
vg0434560709 NA 1.86E-08 mr1240 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
vg0434560709 NA 9.03E-09 mr1242 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
vg0434560709 NA 2.37E-06 mr1247 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
vg0434560709 NA 2.11E-10 mr1495 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
vg0434560709 NA 4.02E-10 mr1496 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
vg0434560709 NA 1.58E-06 mr1917 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
vg0434560709 NA 2.48E-07 mr1936 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
vg0434560709 NA 1.90E-09 mr1011_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
vg0434560709 NA 3.09E-06 mr1117_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
vg0434560709 NA 7.18E-08 mr1118_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
vg0434560709 NA 3.11E-07 mr1119_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
vg0434560709 NA 1.25E-07 mr1123_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
vg0434560709 NA 2.59E-07 mr1240_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
vg0434560709 NA 1.66E-07 mr1242_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
vg0434560709 NA 9.28E-06 mr1405_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
vg0434560709 NA 8.73E-08 mr1495_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
vg0434560709 NA 2.28E-08 mr1496_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
vg0434560709 NA 5.80E-07 mr1936_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