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Detailed information for vg0326473364:

Variant ID: vg0326473364 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 26473364
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

AAATAGGTTCTTGACTAGAAGTGCTAGGTGCATTTTTCATAGGAAATTCATTTTCAAAAAATGTGGCATCTCTAGACTCAGTAATTGTACCAACACGCAT[G/A]
TCGGGTACTCCAGAATTAACTATTAAGAACCTATATCCCATACTGTGGATAGCATAACCAAGGAACACACAATCTACGGTCTTTGGTCCTAGTTTACGCT

Reverse complement sequence

AGCGTAAACTAGGACCAAAGACCGTAGATTGTGTGTTCCTTGGTTATGCTATCCACAGTATGGGATATAGGTTCTTAATAGTTAATTCTGGAGTACCCGA[C/T]
ATGCGTGTTGGTACAATTACTGAGTCTAGAGATGCCACATTTTTTGAAAATGAATTTCCTATGAAAAATGCACCTAGCACTTCTAGTCAAGAACCTATTT

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	73.40%	26.40%	0.13%	0.00%	NA
All Indica	2759	55.70%	44.10%	0.22%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	79.00%	20.80%	0.17%	0.00%	NA
Indica II	465	15.10%	84.90%	0.00%	0.00%	NA
Indica III	913	61.10%	38.60%	0.33%	0.00%	NA
Indica Intermediate	786	55.90%	43.90%	0.25%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	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
vg0326473364	G -> A	LOC_Os03g46800.1	synonymous_variant ; p.Asp254Asp; LOW	synonymous_codon	Average:22.711; most accessible tissue: Zhenshan97 flag leaf, score: 51.466	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0326473364	NA	8.79E-06	mr1231	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
vg0326473364	NA	2.48E-09	mr1557	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
vg0326473364	NA	5.82E-06	mr1946	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
vg0326473364	NA	5.08E-08	mr1124_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