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Detailed information for vg0810807387:

Variant ID: vg0810807387 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10807387
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: 218. )

Flanking Sequence (100 bp) in Reference Genome:


ATCCAAAAATCTTAGGGTATATATACCTATTTTTTATCCAAAAATCTTGGGTATACGTCTGAATACCCTTGAATACATACTGGGCTCACCCCGAATGAGC[G/A]
TTTGTGGCTATTTTGGATGTATATATCCCTCATATCTACTCCCTCCGTCCCATAAAAAAGAATCTAGGACCGAATGTGATATATTCTAGTACTATGAATC

Reverse complement sequence

GATTCATAGTACTAGAATATATCACATTCGGTCCTAGATTCTTTTTTATGGGACGGAGGGAGTAGATATGAGGGATATATACATCCAAAATAGCCACAAA[C/T]
GCTCATTCGGGGTGAGCCCAGTATGTATTCAAGGGTATTCAGACGTATACCCAAGATTTTTGGATAAAAAATAGGTATATATACCCTAAGATTTTTGGAT

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 54.00% 45.60% 0.06% 0.36% NA
All Indica  2759 23.80% 75.60% 0.04% 0.54% NA
All Japonica  1512 98.10% 1.90% 0.00% 0.00% NA
Aus  269 95.90% 3.70% 0.00% 0.37% NA
Indica I  595 4.00% 95.30% 0.00% 0.67% NA
Indica II  465 13.80% 86.20% 0.00% 0.00% NA
Indica III  913 41.80% 57.20% 0.11% 0.88% NA
Indica Intermediate  786 23.80% 75.80% 0.00% 0.38% NA
Temperate Japonica  767 97.90% 2.10% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 3.10% 1.04% 0.00% NA
Intermediate  90 67.80% 30.00% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0810807387 G -> A LOC_Os08g17650.1 upstream_gene_variant ; 3545.0bp to feature; MODIFIER silent_mutation Average:47.875; most accessible tissue: Minghui63 root, score: 81.325 N N N N
vg0810807387 G -> A LOC_Os08g17655.1 downstream_gene_variant ; 2081.0bp to feature; MODIFIER silent_mutation Average:47.875; most accessible tissue: Minghui63 root, score: 81.325 N N N N
vg0810807387 G -> A LOC_Os08g17680.1 downstream_gene_variant ; 2924.0bp to feature; MODIFIER silent_mutation Average:47.875; most accessible tissue: Minghui63 root, score: 81.325 N N N N
vg0810807387 G -> A LOC_Os08g17670.1 intron_variant ; MODIFIER silent_mutation Average:47.875; most accessible tissue: Minghui63 root, score: 81.325 N N N N
vg0810807387 G -> DEL N N silent_mutation Average:47.875; most accessible tissue: Minghui63 root, score: 81.325 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810807387 NA 1.87E-11 mr1609 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
vg0810807387 NA 1.44E-11 mr1883 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
vg0810807387 NA 8.67E-10 mr1945 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
vg0810807387 1.13E-06 NA mr1499_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
vg0810807387 NA 1.78E-11 mr1728_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
vg0810807387 NA 1.28E-11 mr1850_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