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Detailed information for vg0227898687:

Variant ID: vg0227898687 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 27898687
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.07, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GGTCGACATCTTGGAATCTCTCAACTACATCAGCAGCAATCTTGTCAGCCGCTTTCTGCGCATCACTGATGAGGTCGAGAGCAGCTTCTTCGCTCGTCCC[A/G]
TCTGCAAAGCCATCAATGGCATCAATGTCAACTCTTGGATAAAGGGATTTGGTCATCGCCAACGCCAGACTCGCTCCCATACTTCCAGCTTCTTTGATGT

Reverse complement sequence

ACATCAAAGAAGCTGGAAGTATGGGAGCGAGTCTGGCGTTGGCGATGACCAAATCCCTTTATCCAAGAGTTGACATTGATGCCATTGATGGCTTTGCAGA[T/C]
GGGACGAGCGAAGAAGCTGCTCTCGACCTCATCAGTGATGCGCAGAAAGCGGCTGACAAGATTGCTGCTGATGTAGTTGAGAGATTCCAAGATGTCGACC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.70% 9.00% 0.30% 0.00% NA
All Indica  2759 92.20% 7.50% 0.29% 0.00% NA
All Japonica  1512 94.60% 5.30% 0.13% 0.00% NA
Aus  269 50.60% 48.00% 1.49% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 93.50% 6.00% 0.43% 0.00% NA
Indica III  913 88.80% 10.80% 0.33% 0.00% NA
Indica Intermediate  786 89.60% 10.10% 0.38% 0.00% NA
Temperate Japonica  767 92.40% 7.30% 0.26% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 92.10% 7.90% 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
vg0227898687 A -> G LOC_Os02g45800.1 synonymous_variant ; p.Asp719Asp; LOW synonymous_codon Average:24.692; most accessible tissue: Zhenshan97 root, score: 41.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0227898687 NA 4.75E-06 mr1152 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
vg0227898687 3.52E-06 7.67E-07 mr1210 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
vg0227898687 5.89E-06 1.32E-06 mr1305 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
vg0227898687 2.10E-06 2.10E-06 mr1480 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
vg0227898687 2.24E-07 1.02E-07 mr1586 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
vg0227898687 NA 3.01E-06 mr1305_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
vg0227898687 NA 1.26E-06 mr1585_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