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Detailed information for vg0430102469:

Variant ID: vg0430102469 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 30102469
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTAACTATTTTAAATTTAAAAATGAATTAATATGATTTTTAAATCAATTTTTTATAGAAAATCTTTTAAAACAACATACCGTTTAGTAGTTTGGGAAGC[G/A]
TGCACGTGGAAAACAAGACAAACTTGTCCAACCACTGTCTAACTTGCTCATTATTTTATTTTTAAATATCTTAACTACTTAAAAAATACATAATTTTCCA

Reverse complement sequence

TGGAAAATTATGTATTTTTTAAGTAGTTAAGATATTTAAAAATAAAATAATGAGCAAGTTAGACAGTGGTTGGACAAGTTTGTCTTGTTTTCCACGTGCA[C/T]
GCTTCCCAAACTACTAAACGGTATGTTGTTTTAAAAGATTTTCTATAAAAAATTGATTTAAAAATCATATTAATTCATTTTTAAATTTAAAATAGTTAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.50% 4.50% 0.00% 0.00% NA
All Indica  2759 97.50% 2.50% 0.00% 0.00% NA
All Japonica  1512 90.90% 9.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 96.10% 3.90% 0.00% 0.00% NA
Indica Intermediate  786 96.80% 3.20% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 76.60% 23.40% 0.00% 0.00% NA
Japonica Intermediate  241 91.70% 8.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0430102469 G -> A LOC_Os04g50880.1 downstream_gene_variant ; 4739.0bp to feature; MODIFIER silent_mutation Average:68.41; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N
vg0430102469 G -> A LOC_Os04g50870-LOC_Os04g50880 intergenic_region ; MODIFIER silent_mutation Average:68.41; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0430102469 NA 1.23E-06 mr1076 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
vg0430102469 NA 1.18E-06 mr1082 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
vg0430102469 9.39E-06 1.09E-08 mr1083 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
vg0430102469 NA 8.35E-07 mr1408 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
vg0430102469 5.81E-06 1.88E-08 mr1560 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
vg0430102469 NA 1.99E-06 mr1082_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
vg0430102469 NA 2.30E-06 mr1226_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