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Detailed information for vg0220479498:

Variant ID: vg0220479498 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20479498
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATCTGTCCGCAGCCCAACATAACTGTACTCCTACTCTGTAATAAAGAAACTTCTGTTGCTGTGATATTCTGTCTTCCTGTGATACCAGCACTGTTTCCT[A/G]
GGACTGGTATCGATTAACAGGTTAATTTGGAGCGTCACGGGCTAGTTCCGTTCGGGGCTAGTTCGGGGCGTGACACCGCGAGACAAATTTATTAAGCCTA

Reverse complement sequence

TAGGCTTAATAAATTTGTCTCGCGGTGTCACGCCCCGAACTAGCCCCGAACGGAACTAGCCCGTGACGCTCCAAATTAACCTGTTAATCGATACCAGTCC[T/C]
AGGAAACAGTGCTGGTATCACAGGAAGACAGAATATCACAGCAACAGAAGTTTCTTTATTACAGAGTAGGAGTACAGTTATGTTGGGCTGCGGACAGATC

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 62.10% 14.00% 12.06% 11.85% NA
All Indica  2759 60.50% 1.00% 19.83% 18.74% NA
All Japonica  1512 66.00% 33.20% 0.46% 0.33% NA
Aus  269 79.90% 5.20% 2.97% 11.90% NA
Indica I  595 40.20% 0.20% 25.55% 34.12% NA
Indica II  465 62.40% 1.10% 18.28% 18.28% NA
Indica III  913 72.30% 1.10% 14.57% 12.05% NA
Indica Intermediate  786 60.90% 1.40% 22.52% 15.14% NA
Temperate Japonica  767 89.70% 9.80% 0.13% 0.39% NA
Tropical Japonica  504 43.80% 55.40% 0.40% 0.40% NA
Japonica Intermediate  241 36.90% 61.40% 1.66% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 51.10% 33.30% 8.89% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0220479498 A -> G LOC_Os02g34240.1 upstream_gene_variant ; 2949.0bp to feature; MODIFIER silent_mutation Average:31.698; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0220479498 A -> G LOC_Os02g34240-LOC_Os02g34250 intergenic_region ; MODIFIER silent_mutation Average:31.698; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0220479498 A -> DEL N N silent_mutation Average:31.698; 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
vg0220479498 NA 8.19E-06 mr1113 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
vg0220479498 6.35E-06 5.98E-08 mr1114 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
vg0220479498 4.20E-06 2.64E-07 mr1116 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
vg0220479498 NA 3.21E-08 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
vg0220479498 NA 3.82E-06 mr1119 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
vg0220479498 NA 1.96E-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
vg0220479498 NA 2.22E-07 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
vg0220479498 8.72E-06 2.01E-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
vg0220479498 NA 4.54E-06 mr1961 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
vg0220479498 5.66E-06 5.66E-06 mr1041_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
vg0220479498 NA 7.37E-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
vg0220479498 2.16E-06 2.16E-06 mr1293_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
vg0220479498 3.11E-06 3.11E-06 mr1294_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
vg0220479498 NA 1.53E-06 mr1428_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
vg0220479498 4.89E-06 4.89E-06 mr1494_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
vg0220479498 1.87E-06 1.87E-06 mr1497_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
vg0220479498 6.88E-06 6.88E-06 mr1814_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
vg0220479498 NA 4.52E-06 mr1851_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
vg0220479498 NA 8.14E-07 mr1894_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
vg0220479498 NA 4.31E-06 mr1992_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