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Detailed information for vg0509824052:

Variant ID: vg0509824052 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 9824052
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAACAGGTTGGCCCGCTATGCTCCCAAGGATGTTCGTACAGATGAAGAGAAACAGGAGAAATTTCTCGAAGGGTTGAATGACGAGTTGTCAGTCCAGC[T/A]
CATCTCTGGTGAATACGAAGACTTCCAAAAGCTAGTCGACAAGGCGATCCGCTTGGAGGACAAGCACCGGAAGATGGAAAGCAAGAAACGCAAGTTGGCT

Reverse complement sequence

AGCCAACTTGCGTTTCTTGCTTTCCATCTTCCGGTGCTTGTCCTCCAAGCGGATCGCCTTGTCGACTAGCTTTTGGAAGTCTTCGTATTCACCAGAGATG[A/T]
GCTGGACTGACAACTCGTCATTCAACCCTTCGAGAAATTTCTCCTGTTTCTCTTCATCTGTACGAACATCCTTGGGAGCATAGCGGGCCAACCTGTTGAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.70%	2.90%	0.40%	0.00%	NA
All Indica	2759	94.30%	5.00%	0.69%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.60%	7.60%	1.85%	0.00%	NA
Indica II	465	93.10%	5.80%	1.08%	0.00%	NA
Indica III	913	97.80%	2.10%	0.11%	0.00%	NA
Indica Intermediate	786	93.80%	6.00%	0.25%	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	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	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
vg0509824052	T -> A	LOC_Os05g17150.1	missense_variant ; p.Leu275His; MODERATE	nonsynonymous_codon ; L275H	Average:52.261; most accessible tissue: Zhenshan97 flag leaf, score: 72.757	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0509824052	3.01E-07	7.57E-12	mr1023_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