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Detailed information for vg0432240299:

Variant ID: vg0432240299 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32240299
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.26, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CCTGTACCTCCGGTTGGCCGATTCTACTGGTATGCCCACCCTTTTTCCCCTGCGACGATAGAATAGCTCTTAGATTAGCAGTCCTGAATTTTGTTCACTT[G/A]
TGTTGATAGGACACACTTCAAACTCAACAGAAAGAAAAAAGAATCTAGTGAAGGTGGTAGTCTAAATTTAGCATGCCTGTTTTTGAACACGACCACCAGG

Reverse complement sequence

CCTGGTGGTCGTGTTCAAAAACAGGCATGCTAAATTTAGACTACCACCTTCACTAGATTCTTTTTTCTTTCTGTTGAGTTTGAAGTGTGTCCTATCAACA[C/T]
AAGTGAACAAAATTCAGGACTGCTAATCTAAGAGCTATTCTATCGTCGCAGGGGAAAAAGGGTGGGCATACCAGTAGAATCGGCCAACCGGAGGTACAGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.30% 43.60% 0.08% 0.00% NA
All Indica  2759 88.30% 11.60% 0.11% 0.00% NA
All Japonica  1512 7.30% 92.70% 0.07% 0.00% NA
Aus  269 22.30% 77.70% 0.00% 0.00% NA
Indica I  595 89.60% 10.40% 0.00% 0.00% NA
Indica II  465 85.20% 14.60% 0.22% 0.00% NA
Indica III  913 92.10% 7.90% 0.00% 0.00% NA
Indica Intermediate  786 84.70% 15.00% 0.25% 0.00% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 17.70% 82.30% 0.00% 0.00% NA
Japonica Intermediate  241 5.00% 94.60% 0.41% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 43.30% 56.70% 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
vg0432240299 G -> A LOC_Os04g54100.1 upstream_gene_variant ; 4600.0bp to feature; MODIFIER silent_mutation Average:70.545; most accessible tissue: Callus, score: 87.743 N N N N
vg0432240299 G -> A LOC_Os04g54120.1 downstream_gene_variant ; 4578.0bp to feature; MODIFIER silent_mutation Average:70.545; most accessible tissue: Callus, score: 87.743 N N N N
vg0432240299 G -> A LOC_Os04g54110.1 intron_variant ; MODIFIER silent_mutation Average:70.545; most accessible tissue: Callus, score: 87.743 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432240299 NA 3.72E-06 mr1498_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
vg0432240299 2.76E-06 1.39E-06 mr1855_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
vg0432240299 NA 1.29E-08 mr1940_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