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Detailed information for vg0807773496:

Variant ID: vg0807773496 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7773496
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.84, G: 0.17, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

ACCACCAGAATCTACAAGCATCAGTATATTCAACCCCTGAATTTTTCCTTGTAACCGAATGGTAGACTGAGAATCAGTACCCTGAACTGCATGAACTGAC[G/A]
TAGCTAACAAGGAAGAATCACTATCTTCAGAAGATATGCCAGCCTGATCCTCATTTGCATTGTCAGGAAATAGTGCAAAGAGCTCCTGAATAGCGTGAAG

Reverse complement sequence

CTTCACGCTATTCAGGAGCTCTTTGCACTATTTCCTGACAATGCAAATGAGGATCAGGCTGGCATATCTTCTGAAGATAGTGATTCTTCCTTGTTAGCTA[C/T]
GTCAGTTCATGCAGTTCAGGGTACTGATTCTCAGTCTACCATTCGGTTACAAGGAAAAATTCAGGGGTTGAATATACTGATGCTTGTAGATTCTGGTGGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.90%	21.90%	0.28%	39.97%	NA
All Indica	2759	34.90%	1.80%	0.36%	62.92%	NA
All Japonica	1512	33.70%	63.40%	0.00%	2.98%	NA
Aus	269	76.20%	0.40%	0.00%	23.42%	NA
Indica I	595	10.40%	2.00%	0.34%	87.23%	NA
Indica II	465	43.20%	4.50%	0.65%	51.61%	NA
Indica III	913	48.60%	0.70%	0.00%	50.71%	NA
Indica Intermediate	786	32.40%	1.50%	0.64%	65.39%	NA
Temperate Japonica	767	39.50%	59.20%	0.00%	1.30%	NA
Tropical Japonica	504	20.40%	75.20%	0.00%	4.37%	NA
Japonica Intermediate	241	42.70%	51.90%	0.00%	5.39%	NA
VI/Aromatic	96	83.30%	0.00%	0.00%	16.67%	NA
Intermediate	90	37.80%	26.70%	3.33%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0807773496	G -> A	LOC_Os08g13080.1	missense_variant ; p.Thr437Met; MODERATE	nonsynonymous_codon ; T437M	Average:18.756; most accessible tissue: Minghui63 young leaf, score: 35.334	unknown	unknown	DELETERIOUS	0.05
vg0807773496	G -> DEL	LOC_Os08g13080.1	N	frameshift_variant	Average:18.756; most accessible tissue: Minghui63 young leaf, score: 35.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807773496	NA	9.93E-06	mr1036	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
vg0807773496	3.02E-06	NA	mr1105	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