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Detailed information for vg0816476794:

Variant ID: vg0816476794 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16476794
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAGAGATTTTAATCTATCAATTTCAGATTTAAGAGATTCAATGATAAATTCCTGTTTTCTATACATCTTCTCACACTTCATATTTTTTGCACTCAAAA[T/C]
ATTAATAGCTTCTTCAAAAGCACTTACCTCATGATCTTCATACTCAATATCCGATTCACCACGCGCCATGAAGCAAACACCGGAGATGTTCTTTCCCTTA

Reverse complement sequence

TAAGGGAAAGAACATCTCCGGTGTTTGCTTCATGGCGCGTGGTGAATCGGATATTGAGTATGAAGATCATGAGGTAAGTGCTTTTGAAGAAGCTATTAAT[A/G]
TTTTGAGTGCAAAAAATATGAAGTGTGAGAAGATGTATAGAAAACAGGAATTTATCATTGAATCTCTTAAATCTGAAATTGATAGATTAAAATCTCTTAT

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	75.60%	4.10%	9.08%	11.19%	NA
All Indica	2759	65.70%	5.10%	13.99%	15.19%	NA
All Japonica	1512	94.60%	0.40%	0.26%	4.76%	NA
Aus	269	60.20%	16.70%	10.41%	12.64%	NA
Indica I	595	75.00%	1.50%	17.65%	5.88%	NA
Indica II	465	60.00%	6.20%	16.56%	17.20%	NA
Indica III	913	60.70%	7.80%	10.19%	21.36%	NA
Indica Intermediate	786	67.90%	4.10%	14.12%	13.87%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	88.90%	1.20%	0.40%	9.52%	NA
Japonica Intermediate	241	89.60%	0.00%	0.41%	9.96%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	83.30%	1.10%	11.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816476794	T -> C	LOC_Os08g26970.1	missense_variant ; p.Ile389Val; MODERATE	nonsynonymous_codon ; I389V	Average:20.749; most accessible tissue: Zhenshan97 flag leaf, score: 27.583	benign	-0.032	TOLERATED	0.32
vg0816476794	T -> DEL	LOC_Os08g26970.1	N	frameshift_variant	Average:20.749; most accessible tissue: Zhenshan97 flag leaf, score: 27.583	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816476794	4.98E-06	NA	mr1521_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