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Detailed information for vg0819478065:

Variant ID: vg0819478065 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19478065
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGATATTTCATATTTAAGTTTTTTCAAATAAGTTGTTCCTGTGCATGTACTCTCCGTCCTCTAATATAAGGGATTTTGATATTTTTCTTGTACTGTTT[T/C]
ACCATTCATCTTATTAAAAAAATTTGAAATTATTATTTATTTTATTTGTGACCTACTTTATTATCCAAAGTACTTTAAGCACAACTTTTCGGTTTAATAT

Reverse complement sequence

ATATTAAACCGAAAAGTTGTGCTTAAAGTACTTTGGATAATAAAGTAGGTCACAAATAAAATAAATAATAATTTCAAATTTTTTTAATAAGATGAATGGT[A/G]
AAACAGTACAAGAAAAATATCAAAATCCCTTATATTAGAGGACGGAGAGTACATGCACAGGAACAACTTATTTGAAAAAACTTAAATATGAAATATCTCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.50% 29.50% 0.02% 0.00% NA
All Indica  2759 98.30% 1.70% 0.00% 0.00% NA
All Japonica  1512 18.50% 81.50% 0.07% 0.00% NA
Aus  269 83.30% 16.70% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 97.30% 2.70% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 0.80% 99.20% 0.00% 0.00% NA
Tropical Japonica  504 47.20% 52.60% 0.20% 0.00% NA
Japonica Intermediate  241 14.50% 85.50% 0.00% 0.00% NA
VI/Aromatic  96 55.20% 44.80% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 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
vg0819478065 T -> C LOC_Os08g31480.1 upstream_gene_variant ; 4003.0bp to feature; MODIFIER silent_mutation Average:53.365; most accessible tissue: Minghui63 flag leaf, score: 82.521 N N N N
vg0819478065 T -> C LOC_Os08g31480-LOC_Os08g31510 intergenic_region ; MODIFIER silent_mutation Average:53.365; most accessible tissue: Minghui63 flag leaf, score: 82.521 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819478065 1.57E-06 2.70E-06 mr1073 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
vg0819478065 7.97E-06 3.92E-08 mr1073 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
vg0819478065 NA 1.68E-06 mr1350 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
vg0819478065 NA 7.45E-28 mr1638 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
vg0819478065 NA 1.57E-06 mr1646 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
vg0819478065 NA 6.32E-11 mr1714 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
vg0819478065 NA 6.40E-16 mr1830 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
vg0819478065 NA 1.00E-06 mr1830 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
vg0819478065 4.95E-06 3.00E-10 mr1852 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
vg0819478065 NA 3.33E-06 mr1881 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