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Detailed information for vg0414518378:

Variant ID: vg0414518378 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 14518378
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


AAGAAGTTTGACTTAAAAAAGTCAAACGATTTGGGCTGCGTTTGATTCTACAACAAGAGTTGGATTAAATTTTGAATATTCATGGCACGCTTTTTAAGCT[A/G]
CTAAACGGTGCGTTTCGTGCAAAAACTTTCTATAAGAAAGTTGCTCTAAAATATTATATTAATCTATTTTTTAAGTTTGTAATAATTAAAATTTAATTAA

Reverse complement sequence

TTAATTAAATTTTAATTATTACAAACTTAAAAAATAGATTAATATAATATTTTAGAGCAACTTTCTTATAGAAAGTTTTTGCACGAAACGCACCGTTTAG[T/C]
AGCTTAAAAAGCGTGCCATGAATATTCAAAATTTAATCCAACTCTTGTTGTAGAATCAAACGCAGCCCAAATCGTTTGACTTTTTTAAGTCAAACTTCTT

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 64.50% 12.10% 1.54% 21.86% NA
All Indica  2759 54.90% 11.10% 2.32% 31.71% NA
All Japonica  1512 91.30% 0.30% 0.13% 8.27% NA
Aus  269 3.00% 92.20% 1.86% 2.97% NA
Indica I  595 57.00% 0.20% 0.34% 42.52% NA
Indica II  465 24.10% 23.00% 1.72% 51.18% NA
Indica III  913 76.20% 11.10% 3.61% 9.09% NA
Indica Intermediate  786 46.70% 12.30% 2.67% 38.30% NA
Temperate Japonica  767 91.50% 0.00% 0.00% 8.47% NA
Tropical Japonica  504 92.50% 0.40% 0.20% 6.94% NA
Japonica Intermediate  241 88.40% 0.80% 0.41% 10.37% NA
VI/Aromatic  96 84.40% 7.30% 1.04% 7.29% NA
Intermediate  90 70.00% 8.90% 1.11% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0414518378 A -> DEL N N silent_mutation Average:8.297; most accessible tissue: Minghui63 root, score: 13.235 N N N N
vg0414518378 A -> G LOC_Os04g25130.1 upstream_gene_variant ; 2215.0bp to feature; MODIFIER silent_mutation Average:8.297; most accessible tissue: Minghui63 root, score: 13.235 N N N N
vg0414518378 A -> G LOC_Os04g25130-LOC_Os04g25140 intergenic_region ; MODIFIER silent_mutation Average:8.297; most accessible tissue: Minghui63 root, score: 13.235 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0414518378 NA 5.52E-09 mr1059 Ind_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
vg0414518378 6.42E-06 NA mr1143 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
vg0414518378 NA 4.15E-10 mr1143 Ind_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
vg0414518378 NA 5.61E-09 mr1167 Ind_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
vg0414518378 NA 1.73E-06 mr1291 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
vg0414518378 NA 1.38E-18 mr1557 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
vg0414518378 4.99E-06 NA mr1675 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
vg0414518378 NA 6.66E-10 mr1675 Ind_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
vg0414518378 NA 3.23E-11 mr1846 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
vg0414518378 NA 6.03E-07 mr1950 Ind_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
vg0414518378 8.96E-06 NA mr1969 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
vg0414518378 NA 1.93E-09 mr1969 Ind_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
vg0414518378 NA 1.42E-09 mr1995 Ind_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
vg0414518378 NA 2.09E-06 mr1158_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
vg0414518378 NA 2.87E-07 mr1167_2 Ind_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
vg0414518378 NA 3.08E-17 mr1846_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