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Detailed information for vg0402472610:

Variant ID: vg0402472610 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2472610
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.73, C: 0.27, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTGGATAGTACTACAGCTTGAAGGGGGGGAAGAGGGATTTGGGGATTTTGGATAGTACTGCAGCTTGAAGGGGTTAAGTACAGATGTACCATGCTGCA[C/A]
AAGGATTATATTTGAAATTGTTGTCTACGTAGAGCCCCACGTTGGCAATTATCTCCGGTCAAACGAGGTTTGGATTAGTGTGGTAAATGTGTAATTTTTT

Reverse complement sequence

AAAAAATTACACATTTACCACACTAATCCAAACCTCGTTTGACCGGAGATAATTGCCAACGTGGGGCTCTACGTAGACAACAATTTCAAATATAATCCTT[G/T]
TGCAGCATGGTACATCTGTACTTAACCCCTTCAAGCTGCAGTACTATCCAAAATCCCCAAATCCCTCTTCCCCCCCTTCAAGCTGTAGTACTATCCAAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.10% 23.70% 0.19% 0.00% NA
All Indica  2759 98.40% 1.60% 0.00% 0.00% NA
All Japonica  1512 32.70% 67.10% 0.20% 0.00% NA
Aus  269 97.00% 0.70% 2.23% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 15.40% 84.20% 0.39% 0.00% NA
Tropical Japonica  504 52.00% 48.00% 0.00% 0.00% NA
Japonica Intermediate  241 47.30% 52.70% 0.00% 0.00% NA
VI/Aromatic  96 60.40% 39.60% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0402472610 C -> A LOC_Os04g05040-LOC_Os04g05050 intergenic_region ; MODIFIER silent_mutation Average:48.885; most accessible tissue: Zhenshan97 young leaf, score: 65.804 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402472610 8.22E-06 NA mr1415 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
vg0402472610 8.22E-06 NA mr1567 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
vg0402472610 NA 2.54E-07 mr1798_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
vg0402472610 NA 3.41E-07 mr1837_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
vg0402472610 NA 2.76E-06 mr1840_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