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Detailed information for vg0430792799:

Variant ID: vg0430792799 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 30792799
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


CAGGTACATAAGTCCACTATAGCTTTATCTTATGTTATTAGTATTGTACTGGTATTTTTCCCGACCATCTTGCAATTATTTAAGCTGCAATAGGTTGTTG[C/T]
ATATATACATGCAGCATATTCATAGCCGTGAACACTAAGAGTAGGTTTCTCTGAGTACTCTTATCATCAGGGTATTGAAGAACGCAACTCCAAAATTTTA

Reverse complement sequence

TAAAATTTTGGAGTTGCGTTCTTCAATACCCTGATGATAAGAGTACTCAGAGAAACCTACTCTTAGTGTTCACGGCTATGAATATGCTGCATGTATATAT[G/A]
CAACAACCTATTGCAGCTTAAATAATTGCAAGATGGTCGGGAAAAATACCAGTACAATACTAATAACATAAGATAAAGCTATAGTGGACTTATGTACCTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.60% 3.30% 0.06% 0.00% NA
All Indica  2759 99.20% 0.70% 0.04% 0.00% NA
All Japonica  1512 90.90% 9.00% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 97.80% 2.00% 0.13% 0.00% NA
Temperate Japonica  767 96.70% 3.00% 0.26% 0.00% NA
Tropical Japonica  504 95.00% 5.00% 0.00% 0.00% NA
Japonica Intermediate  241 63.50% 36.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0430792799 C -> T LOC_Os04g51900.1 intron_variant ; MODIFIER silent_mutation Average:39.485; most accessible tissue: Callus, score: 82.461 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0430792799 NA 7.67E-06 mr1064 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
vg0430792799 NA 3.27E-08 mr1534 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
vg0430792799 NA 4.54E-09 mr1745 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
vg0430792799 NA 1.47E-06 mr1064_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
vg0430792799 NA 5.79E-06 mr1113_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
vg0430792799 NA 3.08E-11 mr1745_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