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Detailed information for vg0610633502:

Variant ID: vg0610633502 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 10633502
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCCTTTGACGATTAGTCGCTTGGCGCCAAGTGCGGCTGCATCTCGTATCCCGGCAAGTAGTCCTTCGTATTCTGCAGTGTTATTCGTTGCTCTGAAGTT[A/G]
AGGTGGATTGCGTGTTTGAATTGATCTCCGGATGGAGATGTTAAGATAAATCCAGCGCCTGCTCCTTGGCTATTGAGTGCACCATCGAACGCCATTGTCC

Reverse complement sequence

GGACAATGGCGTTCGATGGTGCACTCAATAGCCAAGGAGCAGGCGCTGGATTTATCTTAACATCTCCATCCGGAGATCAATTCAAACACGCAATCCACCT[T/C]
AACTTCAGAGCAACGAATAACACTGCAGAATACGAAGGACTACTTGCCGGGATACGAGATGCAGCCGCACTTGGCGCCAAGCGACTAATCGTCAAAGGGG

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 58.00% 1.80% 25.92% 14.28% NA
All Indica  2759 65.50% 2.50% 30.23% 1.78% NA
All Japonica  1512 49.70% 0.30% 9.79% 40.21% NA
Aus  269 17.50% 4.50% 77.32% 0.74% NA
Indica I  595 75.30% 2.70% 20.67% 1.34% NA
Indica II  465 65.60% 3.70% 30.54% 0.22% NA
Indica III  913 55.30% 1.40% 39.87% 3.40% NA
Indica Intermediate  786 69.80% 2.90% 26.08% 1.15% NA
Temperate Japonica  767 48.80% 0.10% 3.91% 47.20% NA
Tropical Japonica  504 54.80% 0.60% 17.46% 27.18% NA
Japonica Intermediate  241 42.30% 0.00% 12.45% 45.23% NA
VI/Aromatic  96 75.00% 0.00% 17.71% 7.29% NA
Intermediate  90 68.90% 1.10% 20.00% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0610633502 A -> G LOC_Os06g18750.1 downstream_gene_variant ; 2280.0bp to feature; MODIFIER silent_mutation Average:20.399; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N
vg0610633502 A -> G LOC_Os06g18750-LOC_Os06g18770 intergenic_region ; MODIFIER silent_mutation Average:20.399; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N
vg0610633502 A -> DEL N N silent_mutation Average:20.399; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0610633502 1.88E-11 NA mr1087 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
vg0610633502 1.70E-07 5.84E-10 mr1087 Ind_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
vg0610633502 NA 2.19E-07 mr1087 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
vg0610633502 2.25E-07 NA mr1096 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
vg0610633502 2.32E-06 NA mr1110 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
vg0610633502 1.65E-06 NA mr1112 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
vg0610633502 NA 3.19E-06 mr1844 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
vg0610633502 8.07E-06 1.17E-07 mr1078_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
vg0610633502 2.47E-10 NA mr1087_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
vg0610633502 5.50E-06 1.05E-10 mr1087_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
vg0610633502 NA 9.91E-07 mr1090_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
vg0610633502 NA 4.38E-06 mr1096_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