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Detailed information for vg0807428797:

Variant ID: vg0807428797 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7428797
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.07, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

CGCGACCGACGCGAACCTGATTTCCAGATTAAGCCCTTCGCACATTTCTCTGAACTTGTTAGAGTCGAACTGCTTGCCGTTGTCAGTGATGAACTCTTTT[G/A]
GCACTCCGAAACGGCAAATAATGTTTTTCCATACAAACTTCTGTACTGCTGCCGAAGTGAATGCTCCGAGGGGTTCGGCCTCAATCCATCGGGAGAAGTA

Reverse complement sequence

TACTTCTCCCGATGGATTGAGGCCGAACCCCTCGGAGCATTCACTTCGGCAGCAGTACAGAAGTTTGTATGGAAAAACATTATTTGCCGTTTCGGAGTGC[C/T]
AAAAGAGTTCATCACTGACAACGGCAAGCAGTTCGACTCTAACAAGTTCAGAGAAATGTGCGAAGGGCTTAATCTGGAAATCAGGTTCGCGTCGGTCGCG

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	55.40%	43.90%	0.25%	0.51%	NA
All Indica	2759	28.80%	70.00%	0.29%	0.87%	NA
All Japonica	1512	97.90%	1.80%	0.26%	0.00%	NA
Aus	269	77.00%	23.00%	0.00%	0.00%	NA
Indica I	595	15.30%	81.70%	0.34%	2.69%	NA
Indica II	465	49.50%	49.70%	0.00%	0.86%	NA
Indica III	913	22.70%	76.80%	0.33%	0.22%	NA
Indica Intermediate	786	34.00%	65.40%	0.38%	0.25%	NA
Temperate Japonica	767	96.90%	2.60%	0.52%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	77.10%	22.90%	0.00%	0.00%	NA
Intermediate	90	66.70%	33.30%	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
vg0807428797	G -> A	LOC_Os08g12550.1	missense_variant ; p.Pro295Leu; MODERATE	nonsynonymous_codon ; P295L	Average:43.929; most accessible tissue: Minghui63 young leaf, score: 75.937	benign	0.945	TOLERATED	0.07
vg0807428797	G -> DEL	LOC_Os08g12550.1	N	frameshift_variant	Average:43.929; most accessible tissue: Minghui63 young leaf, score: 75.937	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807428797	NA	6.04E-06	mr1577	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