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Detailed information for vg0808442319:

Variant ID: vg0808442319 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 8442319
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


AAAAGAGATAAATGAGGAAAAATTTTGAAATGGGTGGGAGGGAAAATAGGGAATACTATTTTCGCGTGCGGCTCTCTTAATAGATACGCACGGGAAAATC[G/A]
GCTCATTTTCCCGTGCGGTCCGTTTAGGAGGACCGCACGAGAAAATCGATTTTCCCATACGGGCAACAGCCCAGCCCCGGTTCCCCTATTTTTCCGTGCA

Reverse complement sequence

TGCACGGAAAAATAGGGGAACCGGGGCTGGGCTGTTGCCCGTATGGGAAAATCGATTTTCTCGTGCGGTCCTCCTAAACGGACCGCACGGGAAAATGAGC[C/T]
GATTTTCCCGTGCGTATCTATTAAGAGAGCCGCACGCGAAAATAGTATTCCCTATTTTCCCTCCCACCCATTTCAAAATTTTTCCTCATTTATCTCTTTT

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 96.80% 3.00% 0.21% 0.00% NA
All Indica  2759 94.90% 5.00% 0.14% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 98.50% 0.00% 1.49% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 75.50% 24.10% 0.43% 0.00% NA
Indica III  913 99.80% 0.10% 0.11% 0.00% NA
Indica Intermediate  786 96.80% 3.10% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 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
vg0808442319 G -> A LOC_Os08g14109.1 intron_variant ; MODIFIER silent_mutation Average:35.859; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0808442319 2.02E-06 NA mr1944_2 Ind_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