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Detailed information for vg0816082604:

Variant ID: vg0816082604 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16082604
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: 0.01, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:


CCTCCATTGGATGTCATGAGGCGCACGCCACCAGTCCTCACTGGCACTTGCCCAGCTTGAGACTCTGATGCTGTGGCGTGGAGCTTGGGTCCATCCTGGT[G/A]
CATCCCCAGTTGGCTCCCAACCTACCTCATACATCTGCATGGGTGTTGAGGATGATGAACTTTCTTGTTCATTCCTTGTCATGTTGCGCGTCTCCCTGTA

Reverse complement sequence

TACAGGGAGACGCGCAACATGACAAGGAATGAACAAGAAAGTTCATCATCCTCAACACCCATGCAGATGTATGAGGTAGGTTGGGAGCCAACTGGGGATG[C/T]
ACCAGGATGGACCCAAGCTCCACGCCACAGCATCAGAGTCTCAAGCTGGGCAAGTGCCAGTGAGGACTGGTGGCGTGCGCCTCATGACATCCAATGGAGG

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 47.90% 3.30% 19.21% 29.64% NA
All Indica  2759 36.80% 5.50% 30.70% 26.93% NA
All Japonica  1512 59.30% 0.00% 1.79% 38.96% NA
Aus  269 76.20% 0.00% 7.43% 16.36% NA
Indica I  595 42.70% 7.20% 37.14% 12.94% NA
Indica II  465 37.60% 6.70% 21.72% 33.98% NA
Indica III  913 30.20% 4.50% 34.28% 31.00% NA
Indica Intermediate  786 39.60% 4.80% 26.97% 28.63% NA
Temperate Japonica  767 96.70% 0.00% 0.26% 3.00% NA
Tropical Japonica  504 11.30% 0.00% 4.17% 84.52% NA
Japonica Intermediate  241 40.20% 0.00% 1.66% 58.09% NA
VI/Aromatic  96 94.80% 0.00% 2.08% 3.12% NA
Intermediate  90 60.00% 2.20% 13.33% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0816082604 G -> A LOC_Os08g26390.1 missense_variant ; p.Ala144Val; MODERATE nonsynonymous_codon ; A144V Average:8.538; most accessible tissue: Minghui63 root, score: 15.664 benign 1.453 DELETERIOUS 0.02
vg0816082604 G -> DEL LOC_Os08g26390.1 N frameshift_variant Average:8.538; most accessible tissue: Minghui63 root, score: 15.664 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816082604 NA 2.20E-06 mr1230 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
vg0816082604 3.62E-06 3.62E-06 mr1230 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