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Detailed information for vg0413423284:

Variant ID: vg0413423284 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 13423284
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


AACATTATTTGCCGTTTCGGAGTGCCGAAAGAGTTCATCACTGATAACGGCAAGCAATTCGACTCCAACAAATTCAAAGAAATGTGCAAGGGCTAAACCT[G/A]
GAAATCAGGTTCGCCTCAGTCGCGCACCCACAGTCAAATGGGGCGGCTGAGCGCACAAATGGCAAAATTCTTGAGGTGCTCAAAAAAAGGCTTGAGGGGG

Reverse complement sequence

CCCCCTCAAGCCTTTTTTTGAGCACCTCAAGAATTTTGCCATTTGTGCGCTCAGCCGCCCCATTTGACTGTGGGTGCGCGACTGAGGCGAACCTGATTTC[C/T]
AGGTTTAGCCCTTGCACATTTCTTTGAATTTGTTGGAGTCGAATTGCTTGCCGTTATCAGTGATGAACTCTTTCGGCACTCCGAAACGGCAAATAATGTT

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 90.50% 5.70% 0.06% 3.72% NA
All Indica  2759 99.70% 0.20% 0.00% 0.11% NA
All Japonica  1512 71.80% 16.70% 0.20% 11.31% 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 98.90% 0.90% 0.00% 0.22% NA
Indica III  913 99.90% 0.00% 0.00% 0.11% NA
Indica Intermediate  786 99.60% 0.30% 0.00% 0.13% NA
Temperate Japonica  767 97.70% 2.10% 0.00% 0.26% NA
Tropical Japonica  504 28.40% 40.10% 0.40% 31.15% NA
Japonica Intermediate  241 80.50% 14.10% 0.41% 4.98% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 88.90% 8.90% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0413423284 G -> DEL LOC_Os04g23480.1 N frameshift_variant Average:52.796; most accessible tissue: Minghui63 young leaf, score: 75.937 N N N N
vg0413423284 G -> A LOC_Os04g23480.1 synonymous_variant ; p.Leu239Leu; LOW synonymous_codon Average:52.796; most accessible tissue: Minghui63 young leaf, score: 75.937 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0413423284 NA 5.66E-06 mr1213 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
vg0413423284 NA 2.73E-07 mr1248 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
vg0413423284 NA 6.61E-09 mr1248 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
vg0413423284 NA 5.70E-06 mr1295 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
vg0413423284 NA 1.21E-20 mr1301 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
vg0413423284 9.31E-10 6.65E-22 mr1410 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
vg0413423284 NA 1.01E-12 mr1410 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
vg0413423284 NA 2.63E-06 mr1471 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
vg0413423284 NA 2.63E-08 mr1642 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
vg0413423284 NA 1.83E-06 mr1642 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
vg0413423284 NA 8.04E-08 mr1668 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
vg0413423284 NA 2.63E-11 mr1864 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
vg0413423284 NA 2.02E-09 mr1980 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
vg0413423284 NA 7.59E-06 mr1246_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
vg0413423284 NA 1.30E-22 mr1301_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
vg0413423284 6.33E-07 3.19E-21 mr1410_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
vg0413423284 NA 1.08E-11 mr1410_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
vg0413423284 NA 5.01E-06 mr1574_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
vg0413423284 NA 6.97E-07 mr1786_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