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Detailed information for vg0919476706:

Variant ID: vg0919476706 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19476706
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


TCCAGAAGCTCTGCATGCCTTTCATCAAGTCGAAAAAAGATGAGGCGAGGAGTGTTGGGCCCCACGCTTTGAATTTGAAGCTTCCTTTTGGTGAAATGAG[T/A]
GTTCTCGAGGAGAACTTGGAGCTGATCAAGAGGCAGGTAGGCCTTGAACATGCAGAGGTCCTGTCTGCTTCTGATGAGGCTGCTCGTGCTAAAGCTGGCG

Reverse complement sequence

CGCCAGCTTTAGCACGAGCAGCCTCATCAGAAGCAGACAGGACCTCTGCATGTTCAAGGCCTACCTGCCTCTTGATCAGCTCCAAGTTCTCCTCGAGAAC[A/T]
CTCATTTCACCAAAAGGAAGCTTCAAATTCAAAGCGTGGGGCCCAACACTCCTCGCCTCATCTTTTTTCGACTTGATGAAAGGCATGCAGAGCTTCTGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.60% 5.00% 1.40% 0.00% NA
All Indica  2759 90.00% 7.80% 2.21% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 94.40% 4.10% 1.49% 0.00% NA
Indica I  595 63.40% 27.60% 9.08% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 97.40% 2.60% 0.00% 0.00% NA
Indica Intermediate  786 95.80% 3.30% 0.89% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 8.30% 1.04% 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
vg0919476706 T -> A LOC_Os09g32650.1 missense_variant ; p.Ser1032Arg; MODERATE nonsynonymous_codon ; S1032R Average:67.062; most accessible tissue: Minghui63 flag leaf, score: 76.091 unknown unknown TOLERATED 0.14

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919476706 1.20E-07 NA mr1389 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
vg0919476706 3.33E-06 NA mr1389 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
vg0919476706 2.75E-06 NA mr1038_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
vg0919476706 2.26E-07 NA mr1389_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
vg0919476706 1.08E-06 NA mr1389_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
vg0919476706 NA 6.21E-07 mr1904_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