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Detailed information for vg0107990856:

Variant ID: vg0107990856 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7990856
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.23, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


TCGATATGAATGTCACTAGAACGGATACCCTCATCTCAATCGGGCGGTAAGCCCCATCTCAATCGGGCATGGCGTCCGTCACAGGCTAGAAGTCACTGAT[G/A]
TGAAGAGCTATTTCAATCGGGCAAACGGCTGTCACGGATGATTCTATCTCAATCGGGCCCTAAGTAAAGCCCGTCACCGATAGCTTTGACCCAGACGACC

Reverse complement sequence

GGTCGTCTGGGTCAAAGCTATCGGTGACGGGCTTTACTTAGGGCCCGATTGAGATAGAATCATCCGTGACAGCCGTTTGCCCGATTGAAATAGCTCTTCA[C/T]
ATCAGTGACTTCTAGCCTGTGACGGACGCCATGCCCGATTGAGATGGGGCTTACCGCCCGATTGAGATGAGGGTATCCGTTCTAGTGACATTCATATCGA

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 92.90% 6.70% 0.38% 0.00% NA
All Indica  2759 95.70% 3.90% 0.43% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 20.80% 77.00% 2.23% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.80% 1.90% 0.22% 0.00% NA
Indica III  913 93.00% 6.40% 0.66% 0.00% NA
Indica Intermediate  786 94.30% 5.10% 0.64% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0107990856 G -> A LOC_Os01g14250.1 upstream_gene_variant ; 754.0bp to feature; MODIFIER silent_mutation Average:41.814; most accessible tissue: Zhenshan97 root, score: 66.982 N N N N
vg0107990856 G -> A LOC_Os01g14260.1 upstream_gene_variant ; 2184.0bp to feature; MODIFIER silent_mutation Average:41.814; most accessible tissue: Zhenshan97 root, score: 66.982 N N N N
vg0107990856 G -> A LOC_Os01g14250-LOC_Os01g14260 intergenic_region ; MODIFIER silent_mutation Average:41.814; most accessible tissue: Zhenshan97 root, score: 66.982 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107990856 NA 4.43E-07 mr1382 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
vg0107990856 2.46E-06 NA mr1593_2 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
vg0107990856 NA 3.93E-06 mr1740_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