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Detailed information for vg0400996445:

Variant ID: vg0400996445 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 996445
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGAAACCATCTATACACAAGAAACAAGAATAAAAATAAGGGGATAGTTGAATAAAATGAGAGAGAAGAGAAATGATTGGGTGAGAATTTGATTTTAAGA[C/T]
AACATCCATTGGGCATATAGTTTCTATATATAGTATCTGCATGATATGATAAGTATGAAAACTACTCCCTTCGTTTCAGGTTATAAGACGTTTTGACTTT

Reverse complement sequence

AAAGTCAAAACGTCTTATAACCTGAAACGAAGGGAGTAGTTTTCATACTTATCATATCATGCAGATACTATATATAGAAACTATATGCCCAATGGATGTT[G/A]
TCTTAAAATCAAATTCTCACCCAATCATTTCTCTTCTCTCTCATTTTATTCAACTATCCCCTTATTTTTATTCTTGTTTCTTGTGTATAGATGGTTTCTT

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 91.60% 8.10% 0.30% 0.00% NA
All Indica  2759 95.10% 4.30% 0.51% 0.00% NA
All Japonica  1512 87.40% 12.60% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 88.40% 10.20% 1.42% 0.00% NA
Indica Intermediate  786 97.10% 2.80% 0.13% 0.00% NA
Temperate Japonica  767 87.00% 13.00% 0.00% 0.00% NA
Tropical Japonica  504 92.90% 7.10% 0.00% 0.00% NA
Japonica Intermediate  241 77.20% 22.80% 0.00% 0.00% NA
VI/Aromatic  96 36.50% 63.50% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0400996445 C -> T LOC_Os04g02640.1 upstream_gene_variant ; 859.0bp to feature; MODIFIER silent_mutation Average:34.4; most accessible tissue: Callus, score: 63.246 N N N N
vg0400996445 C -> T LOC_Os04g02630.1 downstream_gene_variant ; 3922.0bp to feature; MODIFIER silent_mutation Average:34.4; most accessible tissue: Callus, score: 63.246 N N N N
vg0400996445 C -> T LOC_Os04g02650.1 downstream_gene_variant ; 3195.0bp to feature; MODIFIER silent_mutation Average:34.4; most accessible tissue: Callus, score: 63.246 N N N N
vg0400996445 C -> T LOC_Os04g02630-LOC_Os04g02640 intergenic_region ; MODIFIER silent_mutation Average:34.4; most accessible tissue: Callus, score: 63.246 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0400996445 NA 3.00E-06 mr1043_2 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
vg0400996445 3.95E-06 NA mr1667_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
vg0400996445 6.35E-07 NA mr1698_2 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