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Detailed information for vg1016294522:

Variant ID: vg1016294522 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 16294522
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.83, T: 0.17, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:

AGCGTAAGTTGGAGGTTCTAATTTCACCAAACCCGACAAAGCGGGGGAGAATCGGATGTAACTTTTTCTGTAGATGTCCATAGATATATTATTTGCCTGA[T/A]
TTCAGGTCCGTGTGAGAAAGTTACGCTTATTTTAAGAAATAACACCCGAATGAAAAAAAAATATACAAACCCGAACTTTTTTATAGGTAATAAAAGATGT

Reverse complement sequence

ACATCTTTTATTACCTATAAAAAAGTTCGGGTTTGTATATTTTTTTTTCATTCGGGTGTTATTTCTTAAAATAAGCGTAACTTTCTCACACGGACCTGAA[A/T]
TCAGGCAAATAATATATCTATGGACATCTACAGAAAAAGTTACATCCGATTCTCCCCCGCTTTGTCGGGTTTGGTGAAATTAGAACCTCCAACTTACGCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.00%	26.30%	0.17%	16.55%	NA
All Indica	2759	90.80%	8.40%	0.22%	0.58%	NA
All Japonica	1512	5.60%	47.30%	0.13%	46.96%	NA
Aus	269	8.20%	77.00%	0.00%	14.87%	NA
Indica I	595	80.70%	19.00%	0.17%	0.17%	NA
Indica II	465	94.80%	4.30%	0.22%	0.65%	NA
Indica III	913	95.20%	4.70%	0.11%	0.00%	NA
Indica Intermediate	786	91.10%	7.00%	0.38%	1.53%	NA
Temperate Japonica	767	1.80%	85.30%	0.00%	12.91%	NA
Tropical Japonica	504	6.30%	2.80%	0.40%	90.48%	NA
Japonica Intermediate	241	16.20%	19.50%	0.00%	64.32%	NA
VI/Aromatic	96	32.30%	64.60%	0.00%	3.12%	NA
Intermediate	90	56.70%	28.90%	0.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1016294522	T -> A	LOC_Os10g31120.1	upstream_gene_variant ; 358.0bp to feature; MODIFIER	silent_mutation	Average:26.835; most accessible tissue: Callus, score: 53.632	N	N	N	N
vg1016294522	T -> A	LOC_Os10g31130.1	upstream_gene_variant ; 3072.0bp to feature; MODIFIER	silent_mutation	Average:26.835; most accessible tissue: Callus, score: 53.632	N	N	N	N
vg1016294522	T -> A	LOC_Os10g31110.1	downstream_gene_variant ; 3541.0bp to feature; MODIFIER	silent_mutation	Average:26.835; most accessible tissue: Callus, score: 53.632	N	N	N	N
vg1016294522	T -> A	LOC_Os10g31110-LOC_Os10g31120	intergenic_region ; MODIFIER	silent_mutation	Average:26.835; most accessible tissue: Callus, score: 53.632	N	N	N	N
vg1016294522	T -> DEL	N	N	silent_mutation	Average:26.835; most accessible tissue: Callus, score: 53.632	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1016294522	NA	2.61E-13	mr1013	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
vg1016294522	NA	1.24E-07	mr1045	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
vg1016294522	NA	1.40E-07	mr1530	Jap_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
vg1016294522	8.03E-07	8.03E-07	mr1181_2	Jap_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
vg1016294522	NA	3.15E-08	mr1585_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