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Detailed information for vg0229409337:

Variant ID: vg0229409337 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 29409337
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CGTATAGATACGCATTTTTTTTCGTTTACCCCATAAAACTTCTTCAAAATCGATGTAATGGAATCCTAGTACGTATTATGTCCCATACAACGAGGACATC[C/G]
AAACACAAAGCTCTGTATTACAGGTATTAAAACCAATCACGGAGCATAATTACATGAAGTCAAAACAACACAGCTACACACCCCCATGATCATACTTAAT

Reverse complement sequence

ATTAAGTATGATCATGGGGGTGTGTAGCTGTGTTGTTTTGACTTCATGTAATTATGCTCCGTGATTGGTTTTAATACCTGTAATACAGAGCTTTGTGTTT[G/C]
GATGTCCTCGTTGTATGGGACATAATACGTACTAGGATTCCATTACATCGATTTTGAAGAAGTTTTATGGGGTAAACGAAAAAAAATGCGTATCTATACG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.60% 6.30% 0.02% 0.00% NA
All Indica  2759 89.30% 10.60% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 82.40% 17.60% 0.00% 0.00% NA
Indica II  465 83.90% 16.10% 0.00% 0.00% NA
Indica III  913 95.70% 4.20% 0.11% 0.00% NA
Indica Intermediate  786 90.50% 9.50% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0229409337 C -> G LOC_Os02g48040.1 upstream_gene_variant ; 2302.0bp to feature; MODIFIER silent_mutation Average:46.896; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0229409337 C -> G LOC_Os02g48040-LOC_Os02g48050 intergenic_region ; MODIFIER silent_mutation Average:46.896; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0229409337 4.76E-06 NA mr1373_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
vg0229409337 NA 5.86E-06 mr1389_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
vg0229409337 NA 2.07E-06 mr1389_2 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