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Detailed information for vg0305879043:

Variant ID: vg0305879043 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 5879043
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAATTGCCATTGGGATTGGTAACTCTGCCATGAAGATTGTTGCTGGGTTAGTTGAAAGTGTACGTTTTTGGTGTTTTCAGGTGTTTAGTGCTAGCTTCG[A/T]
GGAATGATCTTAGGTGCTTGTAGGATGGTGTTTTCAGTATGAACCCTTTCTTTAGTTGATGTGTATCTCTTTTTTATCAATGAAATGAGGCAGAACTTCT

Reverse complement sequence

AGAAGTTCTGCCTCATTTCATTGATAAAAAAGAGATACACATCAACTAAAGAAAGGGTTCATACTGAAAACACCATCCTACAAGCACCTAAGATCATTCC[T/A]
CGAAGCTAGCACTAAACACCTGAAAACACCAAAAACGTACACTTTCAACTAACCCAGCAACAATCTTCATGGCAGAGTTACCAATCCCAATGGCAATTTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.10% 4.90% 0.02% 0.00% NA
All Indica  2759 98.90% 1.00% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 27.10% 72.90% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0305879043 A -> T LOC_Os03g11410.1 downstream_gene_variant ; 4227.0bp to feature; MODIFIER silent_mutation Average:40.1; most accessible tissue: Callus, score: 79.199 N N N N
vg0305879043 A -> T LOC_Os03g11420.1 intron_variant ; MODIFIER silent_mutation Average:40.1; most accessible tissue: Callus, score: 79.199 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0305879043 NA 3.50E-06 mr1126 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
vg0305879043 NA 2.34E-06 mr1262 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
vg0305879043 NA 2.31E-06 mr1474 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
vg0305879043 NA 2.31E-06 mr1475 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
vg0305879043 1.60E-08 5.02E-49 mr1549 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
vg0305879043 5.82E-09 1.40E-51 mr1550 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
vg0305879043 NA 2.96E-46 mr1757 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
vg0305879043 NA 4.10E-07 mr1762 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
vg0305879043 NA 7.74E-38 mr1549_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
vg0305879043 6.47E-07 8.15E-54 mr1550_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
vg0305879043 2.94E-06 2.30E-34 mr1757_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
vg0305879043 NA 1.52E-07 mr1762_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