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Detailed information for vg0423691960:

Variant ID: vg0423691960 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 23691960
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGTCTAAGGCTATATTACACTTTTCCCTAAGATGACAATCGCAGGATACAAAGACTACCAAGAAGGCCAACGCCAGTCCATAGATTGTAAGACCTTCTC[C/T]
GCCAACGACACCATCGACTTCGCCAGGTGGTCTATCTCCGCCGGAGTCCTCCGAGAACGAGCAAAACCTTCACGGAGAAAATCGAGGTCCAGTCGCGGGC

Reverse complement sequence

GCCCGCGACTGGACCTCGATTTTCTCCGTGAAGGTTTTGCTCGTTCTCGGAGGACTCCGGCGGAGATAGACCACCTGGCGAAGTCGATGGTGTCGTTGGC[G/A]
GAGAAGGTCTTACAATCTATGGACTGGCGTTGGCCTTCTTGGTAGTCTTTGTATCCTGCGATTGTCATCTTAGGGAAAAGTGTAATATAGCCTTAGACTT

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 99.10% 0.60% 0.36% 0.00% NA
All Indica  2759 99.90% 0.00% 0.11% 0.00% NA
All Japonica  1512 97.40% 1.70% 0.93% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 95.80% 2.70% 1.43% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 97.10% 2.10% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0423691960 C -> T LOC_Os04g39760.1 synonymous_variant ; p.Ala586Ala; LOW synonymous_codon Average:47.407; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0423691960 2.73E-07 1.22E-09 mr1549_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
vg0423691960 NA 5.68E-06 mr1550_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
vg0423691960 NA 1.61E-07 mr1757_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