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Detailed information for vg0404665726:

Variant ID: vg0404665726 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4665726
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


CATAATCGAAATAGGCAGCAACCGCTAAAACAATCCGAATAGATTTTAGCATGGCGGCTGGCGAGAAAGTTTCATCATAATCAACACCTTGAATTTGTCT[G/A]
AAACCTTTCACCACCAATCGTGCCTTGTAGATGTAAACATTTCCATCTACATCTGTCTTTTTCTTAAAGACCTATTTGCACTCAATGGCTTTTACACCAT

Reverse complement sequence

ATGGTGTAAAAGCCATTGAGTGCAAATAGGTCTTTAAGAAAAAGACAGATGTAGATGGAAATGTTTACATCTACAAGGCACGATTGGTGGTGAAAGGTTT[C/T]
AGACAAATTCAAGGTGTTGATTATGATGAAACTTTCTCGCCAGCCGCCATGCTAAAATCTATTCGGATTGTTTTAGCGGTTGCTGCCTATTTCGATTATG

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 88.90% 10.30% 0.80% 0.00% NA
All Indica  2759 83.70% 15.20% 1.16% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 80.30% 17.80% 1.86% 0.00% NA
Indica I  595 97.30% 1.50% 1.18% 0.00% NA
Indica II  465 55.50% 41.90% 2.58% 0.00% NA
Indica III  913 90.70% 8.90% 0.44% 0.00% NA
Indica Intermediate  786 81.90% 16.90% 1.15% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 1.11% 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
vg0404665726 G -> A LOC_Os04g08580.1 synonymous_variant ; p.Phe576Phe; LOW synonymous_codon Average:16.251; most accessible tissue: Callus, score: 29.3 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404665726 NA 1.90E-06 mr1062_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
vg0404665726 NA 1.89E-06 mr1608_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
vg0404665726 NA 9.32E-06 mr1871_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
vg0404665726 2.24E-06 NA mr1907_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
vg0404665726 2.75E-06 NA mr1934_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