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Detailed information for vg1016628494:

Variant ID: vg1016628494 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 16628494
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

GAAATAATGGAAATTTTCAACACAGAAATCACAAAAAAAATTCGTATGCACTTATAAGTAAAGACTCTTATTAGGTTGCATGCTTAGAAGAAGTAGGGAT[G/A]
TGAAAATTAGAGTTTAATCCTATTAAACATAGTGGATTGTAGGTTGTATTTAGACTTTTTTTTTGATAATTCGGTCTTTTCGGTCTATTCGGTTACCCGA

Reverse complement sequence

TCGGGTAACCGAATAGACCGAAAAGACCGAATTATCAAAAAAAAAGTCTAAATACAACCTACAATCCACTATGTTTAATAGGATTAAACTCTAATTTTCA[C/T]
ATCCCTACTTCTTCTAAGCATGCAACCTAATAAGAGTCTTTACTTATAAGTGCATACGAATTTTTTTTGTGATTTCTGTGTTGAAAATTTCCATTATTTC

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	34.80%	5.50%	15.70%	43.91%	NA
All Indica	2759	6.20%	9.50%	26.06%	58.32%	NA
All Japonica	1512	92.50%	0.10%	0.33%	7.14%	NA
Aus	269	1.10%	0.00%	1.86%	97.03%	NA
Indica I	595	5.90%	2.00%	23.53%	68.57%	NA
Indica II	465	6.90%	13.80%	25.59%	53.76%	NA
Indica III	913	4.80%	12.20%	28.81%	54.22%	NA
Indica Intermediate	786	7.50%	9.40%	25.06%	58.02%	NA
Temperate Japonica	767	98.00%	0.00%	0.26%	1.69%	NA
Tropical Japonica	504	93.80%	0.00%	0.20%	5.95%	NA
Japonica Intermediate	241	71.80%	0.40%	0.83%	26.97%	NA
VI/Aromatic	96	32.30%	0.00%	2.08%	65.62%	NA
Intermediate	90	50.00%	0.00%	12.22%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1016628494	G -> A	LOC_Os10g31720.1	upstream_gene_variant ; 1921.0bp to feature; MODIFIER	silent_mutation	Average:10.576; most accessible tissue: Callus, score: 24.829	N	N	N	N
vg1016628494	G -> A	LOC_Os10g31720-LOC_Os10g31730	intergenic_region ; MODIFIER	silent_mutation	Average:10.576; most accessible tissue: Callus, score: 24.829	N	N	N	N
vg1016628494	G -> DEL	N	N	silent_mutation	Average:10.576; most accessible tissue: Callus, score: 24.829	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1016628494	1.37E-06	NA	mr1951	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