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Detailed information for vg0130669509:

Variant ID: vg0130669509 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 30669509
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:


AATAAAAAAGATCCCAAAATTAATAAAAAAAATAAAAAGAAGGGTTCAACTAGAAATACAATTTAGAAAATGACTAAAATTCGAAATAAAAAAAAGAACG[A/G]
CAATGCTAGGGGACGGGATACCGTCCCCCAACGGGATAGCTCCTCTCCACACGCGATTCTTATCCATACACTCACTTGCCGCCGTCGCCGTCCCCCCTTC

Reverse complement sequence

GAAGGGGGGACGGCGACGGCGGCAAGTGAGTGTATGGATAAGAATCGCGTGTGGAGAGGAGCTATCCCGTTGGGGGACGGTATCCCGTCCCCTAGCATTG[T/C]
CGTTCTTTTTTTTATTTCGAATTTTAGTCATTTTCTAAATTGTATTTCTAGTTGAACCCTTCTTTTTATTTTTTTTATTAATTTTGGGATCTTTTTTATT

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 63.60% 34.40% 0.02% 1.93% NA
All Indica  2759 97.90% 2.00% 0.04% 0.04% NA
All Japonica  1512 0.80% 93.30% 0.00% 5.89% NA
Aus  269 95.20% 4.50% 0.00% 0.37% NA
Indica I  595 96.30% 3.40% 0.17% 0.17% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 96.60% 3.40% 0.00% 0.00% NA
Temperate Japonica  767 0.30% 95.30% 0.00% 4.43% NA
Tropical Japonica  504 1.20% 97.20% 0.00% 1.59% NA
Japonica Intermediate  241 1.70% 78.80% 0.00% 19.50% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 33.30% 66.70% 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
vg0130669509 A -> G LOC_Os01g53380.1 upstream_gene_variant ; 2023.0bp to feature; MODIFIER silent_mutation Average:55.494; most accessible tissue: Minghui63 young leaf, score: 67.374 N N N N
vg0130669509 A -> G LOC_Os01g53370.1 downstream_gene_variant ; 878.0bp to feature; MODIFIER silent_mutation Average:55.494; most accessible tissue: Minghui63 young leaf, score: 67.374 N N N N
vg0130669509 A -> G LOC_Os01g53370-LOC_Os01g53380 intergenic_region ; MODIFIER silent_mutation Average:55.494; most accessible tissue: Minghui63 young leaf, score: 67.374 N N N N
vg0130669509 A -> DEL N N silent_mutation Average:55.494; most accessible tissue: Minghui63 young leaf, score: 67.374 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0130669509 NA 6.64E-21 mr1003 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
vg0130669509 NA 6.19E-09 mr1005 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
vg0130669509 2.03E-06 3.29E-116 mr1008 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
vg0130669509 1.67E-06 1.19E-114 mr1009 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
vg0130669509 4.51E-06 2.84E-78 mr1014 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
vg0130669509 NA 1.55E-77 mr1015 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
vg0130669509 NA 9.46E-26 mr1024 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
vg0130669509 NA 5.22E-12 mr1070 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
vg0130669509 NA 2.09E-11 mr1128 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
vg0130669509 NA 1.13E-13 mr1239 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
vg0130669509 NA 2.92E-06 mr1508 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
vg0130669509 NA 1.16E-12 mr1553 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
vg0130669509 NA 8.17E-22 mr1580 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
vg0130669509 NA 6.01E-07 mr1690 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
vg0130669509 NA 2.65E-21 mr1698 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
vg0130669509 NA 9.37E-07 mr1781 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
vg0130669509 NA 9.46E-17 mr1825 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
vg0130669509 NA 5.02E-20 mr1010_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
vg0130669509 NA 1.36E-25 mr1051_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
vg0130669509 NA 1.22E-12 mr1128_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
vg0130669509 NA 1.06E-13 mr1553_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