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Detailed information for vg0315359978:

Variant ID: vg0315359978 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15359978
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: 103. )

Flanking Sequence (100 bp) in Reference Genome:


ATAAAATATCCTAATTAATAGATACAATTGCCTTCCTAGGACTTTATCCATGTATGGCAATTATCTTGAAGTACGTCAACTTAAACCCGATATCGAATAC[A/G]
AGTCGTATTGTCGGAATCGGCTGCATCACTTAACCCAGTCTGACTCGGACTTAGCCGATTCTAATCGTAGCCGATCCGGACTCTAGCCGATTCTTGCTCT

Reverse complement sequence

AGAGCAAGAATCGGCTAGAGTCCGGATCGGCTACGATTAGAATCGGCTAAGTCCGAGTCAGACTGGGTTAAGTGATGCAGCCGATTCCGACAATACGACT[T/C]
GTATTCGATATCGGGTTTAAGTTGACGTACTTCAAGATAATTGCCATACATGGATAAAGTCCTAGGAAGGCAATTGTATCTATTAATTAGGATATTTTAT

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 93.50% 6.00% 0.51% 0.00% NA
All Indica  2759 95.90% 4.00% 0.18% 0.00% NA
All Japonica  1512 91.50% 7.90% 0.66% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 93.10% 6.50% 0.43% 0.00% NA
Indica III  913 91.90% 7.80% 0.33% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 92.20% 7.60% 0.26% 0.00% NA
Tropical Japonica  504 92.90% 7.10% 0.00% 0.00% NA
Japonica Intermediate  241 86.30% 10.40% 3.32% 0.00% NA
VI/Aromatic  96 39.60% 52.10% 8.33% 0.00% NA
Intermediate  90 93.30% 5.60% 1.11% 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
vg0315359978 A -> G LOC_Os03g26890.1 upstream_gene_variant ; 3115.0bp to feature; MODIFIER silent_mutation Average:25.085; most accessible tissue: Zhenshan97 flower, score: 46.765 N N N N
vg0315359978 A -> G LOC_Os03g26900.1 upstream_gene_variant ; 1381.0bp to feature; MODIFIER silent_mutation Average:25.085; most accessible tissue: Zhenshan97 flower, score: 46.765 N N N N
vg0315359978 A -> G LOC_Os03g26900-LOC_Os03g26910 intergenic_region ; MODIFIER silent_mutation Average:25.085; most accessible tissue: Zhenshan97 flower, score: 46.765 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315359978 4.27E-06 NA mr1379 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
vg0315359978 NA 3.61E-07 mr1613_2 Jap_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
vg0315359978 6.30E-08 NA mr1758_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
vg0315359978 NA 6.20E-07 mr1913_2 Jap_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
vg0315359978 NA 8.72E-06 mr1962_2 Jap_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