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Detailed information for vg0202540647:

Variant ID: vg0202540647 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 2540647
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.61, G: 0.38, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


CATTATCAAGAACGTTCTTGACAAATGCAGAGTCGTCGCGCCCAACCAACCAACGAAGACCGACGACCTATCTCATACACCGGCCATGGCTGGACTACTC[G/A]
AGAAAAGGTTGTTAACGGATAATTGCTCACGAACAATGTCGGCTTGATCACCCGACATGATCGCGGACAGACATCCGGATATGCTACGAGTTGGGTATGT

Reverse complement sequence

ACATACCCAACTCGTAGCATATCCGGATGTCTGTCCGCGATCATGTCGGGTGATCAAGCCGACATTGTTCGTGAGCAATTATCCGTTAACAACCTTTTCT[C/T]
GAGTAGTCCAGCCATGGCCGGTGTATGAGATAGGTCGTCGGTCTTCGTTGGTTGGTTGGGCGCGACGACTCTGCATTTGTCAAGAACGTTCTTGATAATG

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 76.60% 23.30% 0.02% 0.00% NA
All Indica  2759 96.30% 3.70% 0.04% 0.00% NA
All Japonica  1512 42.90% 57.10% 0.00% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 95.50% 4.50% 0.00% 0.00% NA
Indica Intermediate  786 93.80% 6.10% 0.13% 0.00% NA
Temperate Japonica  767 8.60% 91.40% 0.00% 0.00% NA
Tropical Japonica  504 89.90% 10.10% 0.00% 0.00% NA
Japonica Intermediate  241 53.90% 46.10% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg0202540647 G -> A LOC_Os02g05290.1 missense_variant ; p.Glu88Lys; MODERATE nonsynonymous_codon ; E88K Average:56.455; most accessible tissue: Minghui63 panicle, score: 74.563 unknown unknown TOLERATED 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0202540647 NA 1.14E-09 mr1712 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
vg0202540647 NA 3.88E-08 mr1770 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
vg0202540647 NA 5.93E-06 mr1826 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
vg0202540647 NA 3.91E-06 mr1977 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
vg0202540647 NA 8.87E-06 mr1840_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