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Detailed information for vg0920504790:

Variant ID: vg0920504790 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20504790
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.24, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:


CTCTAAAGCGATACCGGGAAGTCTCACGCTCCCCCTCTATTTATACATAAGGTAGGCAGCCTAAAGCCACGAACCAAACTCATACTAAGAGTCCTAAACA[C/T]
CTTAGGAAACCCTTTAGTACAAGAAAGAAACTTTACATAACCAATCGTACCAAATTTAGACTCCTTCCAAATTCGACTCCACATCCCATAAGCACACAAT

Reverse complement sequence

ATTGTGTGCTTATGGGATGTGGAGTCGAATTTGGAAGGAGTCTAAATTTGGTACGATTGGTTATGTAAAGTTTCTTTCTTGTACTAAAGGGTTTCCTAAG[G/A]
TGTTTAGGACTCTTAGTATGAGTTTGGTTCGTGGCTTTAGGCTGCCTACCTTATGTATAAATAGAGGGGGAGCGTGAGACTTCCCGGTATCGCTTTAGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.90% 44.10% 0.00% 0.00% NA
All Indica  2759 85.10% 14.90% 0.00% 0.00% NA
All Japonica  1512 0.30% 99.70% 0.00% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 82.40% 17.60% 0.00% 0.00% NA
Indica II  465 92.30% 7.70% 0.00% 0.00% NA
Indica III  913 87.20% 12.80% 0.00% 0.00% NA
Indica Intermediate  786 80.40% 19.60% 0.00% 0.00% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 0.20% 99.80% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 26.70% 73.30% 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
vg0920504790 C -> T LOC_Os09g35640.1 upstream_gene_variant ; 3742.0bp to feature; MODIFIER silent_mutation Average:43.113; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg0920504790 C -> T LOC_Os09g35650.1 downstream_gene_variant ; 1759.0bp to feature; MODIFIER silent_mutation Average:43.113; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg0920504790 C -> T LOC_Os09g35660.1 downstream_gene_variant ; 4907.0bp to feature; MODIFIER silent_mutation Average:43.113; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg0920504790 C -> T LOC_Os09g35640-LOC_Os09g35650 intergenic_region ; MODIFIER silent_mutation Average:43.113; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920504790 NA 5.49E-08 mr1506 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
vg0920504790 NA 1.71E-10 mr1623 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
vg0920504790 NA 8.44E-07 mr1886 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
vg0920504790 9.90E-07 NA mr1728_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
vg0920504790 2.73E-06 NA mr1728_2 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