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Detailed information for vg0305243308:

Variant ID: vg0305243308 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 5243308
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.63, T: 0.37, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

ACGATTCCCAGAAGCTTATTTTGGCACCATTTCCAATCGTTATGGTTGTGGCGGCCGCAAAGAGGAGCTTATCAGTGTCGTCACATGGCATGCCAGAGCC[C/T]
ACCCAAGCTTTTCCGGGTGATTTCCACTCGTGCCAAAGCCAACGCAGCCGTAAGGCTCTTGCGAATTTCTCAAGATTTAGGATGCCCAGGCCTCCAGAAG

Reverse complement sequence

CTTCTGGAGGCCTGGGCATCCTAAATCTTGAGAAATTCGCAAGAGCCTTACGGCTGCGTTGGCTTTGGCACGAGTGGAAATCACCCGGAAAAGCTTGGGT[G/A]
GGCTCTGGCATGCCATGTGACGACACTGATAAGCTCCTCTTTGCGGCCGCCACAACCATAACGATTGGAAATGGTGCCAAAATAAGCTTCTGGGAATCGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.70%	36.50%	23.70%	3.17%	NA
All Indica	2759	55.50%	5.60%	33.56%	5.36%	NA
All Japonica	1512	0.80%	98.90%	0.26%	0.00%	NA
Aus	269	49.40%	4.10%	46.10%	0.37%	NA
Indica I	595	39.20%	1.30%	48.74%	10.76%	NA
Indica II	465	49.70%	6.70%	36.56%	7.10%	NA
Indica III	913	67.30%	9.10%	21.91%	1.75%	NA
Indica Intermediate	786	57.50%	4.20%	33.84%	4.45%	NA
Temperate Japonica	767	0.50%	99.20%	0.26%	0.00%	NA
Tropical Japonica	504	0.80%	99.00%	0.20%	0.00%	NA
Japonica Intermediate	241	1.70%	97.90%	0.41%	0.00%	NA
VI/Aromatic	96	33.30%	14.60%	52.08%	0.00%	NA
Intermediate	90	28.90%	52.20%	17.78%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0305243308	C -> T	LOC_Os03g10280.1	synonymous_variant ; p.Val752Val; LOW	synonymous_codon	Average:36.296; most accessible tissue: Zhenshan97 flower, score: 49.964	N	N	N	N
vg0305243308	C -> DEL	LOC_Os03g10280.1	N	frameshift_variant	Average:36.296; most accessible tissue: Zhenshan97 flower, score: 49.964	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0305243308	NA	5.33E-29	mr1075	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
vg0305243308	NA	2.66E-06	mr1510	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
vg0305243308	4.20E-06	NA	mr1707	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
vg0305243308	NA	2.48E-13	mr1874	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
vg0305243308	NA	1.64E-33	mr1932	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
vg0305243308	NA	6.82E-13	mr1949	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
vg0305243308	NA	2.03E-11	mr1216_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
vg0305243308	NA	4.25E-12	mr1258_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
vg0305243308	NA	2.06E-80	mr1711_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
vg0305243308	NA	4.96E-18	mr1817_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