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Detailed information for vg0405839288:

Variant ID: vg0405839288 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5839288
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.84, T: 0.16, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


GAAAGCAGGCGAAAACCCTGCAAACTTCAATTGCAGATTGGAGAACATCTCCATCCAAAATCCAAACGAAGGCCATGGGAGGTTCGCCGCCCCCGGATTA[A/T]
CCGGAGGGGGATCAACCCTAACCCAAGTCATTGCTTCCATACATGCACGGTTAACACAGCTAATTAATATAACATTGGTCATACAGTGACAGTGATCATA

Reverse complement sequence

TATGATCACTGTCACTGTATGACCAATGTTATATTAATTAGCTGTGTTAACCGTGCATGTATGGAAGCAATGACTTGGGTTAGGGTTGATCCCCCTCCGG[T/A]
TAATCCGGGGGCGGCGAACCTCCCATGGCCTTCGTTTGGATTTTGGATGGAGATGTTCTCCAATCTGCAATTGAAGTTTGCAGGGTTTTCGCCTGCTTTC

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 63.10% 16.40% 0.44% 20.02% NA
All Indica  2759 55.10% 27.50% 0.54% 16.89% NA
All Japonica  1512 82.10% 0.50% 0.13% 17.33% NA
Aus  269 39.40% 0.40% 1.12% 59.11% NA
Indica I  595 76.80% 5.00% 0.67% 17.48% NA
Indica II  465 63.70% 24.10% 0.43% 11.83% NA
Indica III  913 37.50% 46.30% 0.22% 15.99% NA
Indica Intermediate  786 53.90% 24.70% 0.89% 20.48% NA
Temperate Japonica  767 94.00% 0.00% 0.26% 5.74% NA
Tropical Japonica  504 61.30% 1.20% 0.00% 37.50% NA
Japonica Intermediate  241 87.60% 0.40% 0.00% 12.03% NA
VI/Aromatic  96 56.20% 0.00% 0.00% 43.75% NA
Intermediate  90 68.90% 11.10% 1.11% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0405839288 A -> DEL LOC_Os04g10740.1 N frameshift_variant Average:11.401; most accessible tissue: Callus, score: 74.949 N N N N
vg0405839288 A -> T LOC_Os04g10740.1 missense_variant ; p.Val11Asp; MODERATE nonsynonymous_codon ; V11D Average:11.401; most accessible tissue: Callus, score: 74.949 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405839288 NA 3.65E-13 mr1035 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
vg0405839288 NA 5.07E-06 mr1035 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
vg0405839288 NA 1.01E-11 mr1626 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
vg0405839288 NA 8.38E-18 mr1913 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
vg0405839288 NA 1.58E-07 mr1946 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
vg0405839288 NA 6.87E-19 mr1062_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
vg0405839288 1.71E-08 7.59E-09 mr1062_2 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