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Detailed information for vg0805178156:

Variant ID: vg0805178156 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5178156
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.05, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


AATAGTTGATTGAAACTAACATCGCAGGAAAATGTTCTCTACATTTTTCAGTAGCATTATTATTTTTCCATCATGAATATCCCTCGTCAATTGTATGCAC[A/G]
TTTGTATATATGTCATATTTATTAATAAGTTTTTTTTCACACATATAGGTCCAGCTAATCCTGAAGATATGAACGATGTATTTGAGTTCGCCCTGAACAA

Reverse complement sequence

TTGTTCAGGGCGAACTCAAATACATCGTTCATATCTTCAGGATTAGCTGGACCTATATGTGTGAAAAAAAACTTATTAATAAATATGACATATATACAAA[T/C]
GTGCATACAATTGACGAGGGATATTCATGATGGAAAAATAATAATGCTACTGAAAAATGTAGAGAACATTTTCCTGCGATGTTAGTTTCAATCAACTATT

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 89.40% 10.50% 0.06% 0.00% NA
All Indica  2759 82.60% 17.30% 0.07% 0.00% NA
All Japonica  1512 99.60% 0.30% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 96.80% 3.20% 0.00% 0.00% NA
Indica II  465 68.60% 31.40% 0.00% 0.00% NA
Indica III  913 80.10% 19.80% 0.11% 0.00% NA
Indica Intermediate  786 83.20% 16.70% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0805178156 A -> G LOC_Os08g08890.1 upstream_gene_variant ; 4130.0bp to feature; MODIFIER silent_mutation Average:32.243; most accessible tissue: Zhenshan97 young leaf, score: 49.329 N N N N
vg0805178156 A -> G LOC_Os08g08910.1 downstream_gene_variant ; 1691.0bp to feature; MODIFIER silent_mutation Average:32.243; most accessible tissue: Zhenshan97 young leaf, score: 49.329 N N N N
vg0805178156 A -> G LOC_Os08g08900.1 intron_variant ; MODIFIER silent_mutation Average:32.243; most accessible tissue: Zhenshan97 young leaf, score: 49.329 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805178156 NA 4.34E-09 mr1807 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
vg0805178156 NA 3.91E-06 mr1051_2 Ind_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
vg0805178156 NA 7.10E-08 mr1807_2 Ind_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