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Detailed information for vg0118950790:

Variant ID: vg0118950790 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 18950790
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, G: 0.30, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

TGCGCCAGTACACCGTACTGACAGGCACGTTATCCCGCACAACCCAACCGTTGTGACGTACATAGTTCTTGGCGGCTTCTGCCGGGGCACTAGGTCGGCC[A/G]
TCTTCGTCCACTTCCGTTATGATGTGCCGACCCTCAAGCTTCTTCGCGGCACCTCGTTGTCCGCGTGCCCCCTTCTGTCCAGCGGAGGGTTGACTTCCAC

Reverse complement sequence

GTGGAAGTCAACCCTCCGCTGGACAGAAGGGGGCACGCGGACAACGAGGTGCCGCGAAGAAGCTTGAGGGTCGGCACATCATAACGGAAGTGGACGAAGA[T/C]
GGCCGACCTAGTGCCCCGGCAGAAGCCGCCAAGAACTATGTACGTCACAACGGTTGGGTTGTGCGGGATAACGTGCCTGTCAGTACGGTGTACTGGCGCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.60%	40.80%	1.69%	0.00%	NA
All Indica	2759	89.60%	7.50%	2.90%	0.00%	NA
All Japonica	1512	5.20%	94.80%	0.00%	0.00%	NA
Aus	269	49.40%	50.60%	0.00%	0.00%	NA
Indica I	595	99.00%	0.80%	0.17%	0.00%	NA
Indica II	465	83.20%	6.50%	10.32%	0.00%	NA
Indica III	913	88.40%	11.20%	0.44%	0.00%	NA
Indica Intermediate	786	87.50%	9.00%	3.44%	0.00%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	13.70%	86.30%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	38.90%	61.10%	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
vg0118950790	A -> G	LOC_Os01g34374.1	synonymous_variant ; p.Asp1026Asp; LOW	synonymous_codon	Average:34.104; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0118950790	NA	1.72E-20	mr1254	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
vg0118950790	NA	2.56E-06	mr1227_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
vg0118950790	NA	1.40E-06	mr1530_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