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Detailed information for vg1004546341:

Variant ID: vg1004546341 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4546341
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACATAACTTACTCAAGAACGAAATGAAATCTGCATATAGTCAGTAGCAACTAAATTTACATTTTCTGTATGTAATTAATCATATATTGTTTGAAGGGGA[A/G]
ACTTAGTGTAGGATTCATGGGCAATGGCTGAGTTCGACAATATGAGGGGCTTATAATAGGTGTATCCCCAAGCTGAAAACTGAGCAGATTTTTGTAGTGC

Reverse complement sequence

GCACTACAAAAATCTGCTCAGTTTTCAGCTTGGGGATACACCTATTATAAGCCCCTCATATTGTCGAACTCAGCCATTGCCCATGAATCCTACACTAAGT[T/C]
TCCCCTTCAAACAATATATGATTAATTACATACAGAAAATGTAAATTTAGTTGCTACTGACTATATGCAGATTTCATTTCGTTCTTGAGTAAGTTATGTC

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 96.80% 1.50% 0.78% 0.87% NA
All Indica  2759 99.70% 0.00% 0.22% 0.04% NA
All Japonica  1512 92.10% 4.80% 1.06% 2.12% NA
Aus  269 95.90% 0.00% 2.60% 1.49% NA
Indica I  595 99.50% 0.00% 0.34% 0.17% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.80% 0.00% 0.22% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 90.60% 9.40% 0.00% 0.00% NA
Tropical Japonica  504 90.70% 0.00% 3.17% 6.15% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 91.70% 0.00% 4.17% 4.17% NA
Intermediate  90 95.60% 0.00% 4.44% 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
vg1004546341 A -> G LOC_Os10g08370-LOC_Os10g08390 intergenic_region ; MODIFIER silent_mutation Average:31.736; most accessible tissue: Minghui63 young leaf, score: 56.213 N N N N
vg1004546341 A -> DEL N N silent_mutation Average:31.736; most accessible tissue: Minghui63 young leaf, score: 56.213 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004546341 NA 9.53E-07 mr1210 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
vg1004546341 NA 2.40E-06 mr1305 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
vg1004546341 NA 1.37E-08 mr1585 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
vg1004546341 NA 7.27E-07 mr1586 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
vg1004546341 NA 9.95E-06 mr1765 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
vg1004546341 1.28E-07 4.81E-11 mr1305_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
vg1004546341 4.13E-07 4.13E-07 mr1317_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
vg1004546341 9.71E-07 1.78E-08 mr1559_2 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
vg1004546341 1.64E-07 2.33E-13 mr1585_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
vg1004546341 NA 6.69E-06 mr1703_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