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Detailed information for vg1009470579:

Variant ID: vg1009470579 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9470579
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATGTATGTGGGCAATACTAGAAAGCCTTACGTTATAAAACGGAGGGAGTACTTGATTTGATCGGGTATATATACCCATTTGATTTTTCGTATACTCATT[T/A]
AAATTGGGTATATGACCAATTAAATTTTTATACTCACATATCGGGTATGTCTATTTAAAAACAAATTAAATACCATCAAAACACTTATTTTGGGTAAAAA

Reverse complement sequence

TTTTTACCCAAAATAAGTGTTTTGATGGTATTTAATTTGTTTTTAAATAGACATACCCGATATGTGAGTATAAAAATTTAATTGGTCATATACCCAATTT[A/T]
AATGAGTATACGAAAAATCAAATGGGTATATATACCCGATCAAATCAAGTACTCCCTCCGTTTTATAACGTAAGGCTTTCTAGTATTGCCCACATACATA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.50%	4.90%	0.11%	20.50%	NA
All Indica	2759	75.70%	1.20%	0.07%	23.02%	NA
All Japonica	1512	78.90%	0.30%	0.13%	20.63%	NA
Aus	269	38.70%	61.00%	0.00%	0.37%	NA
Indica I	595	98.70%	0.00%	0.00%	1.34%	NA
Indica II	465	78.90%	0.90%	0.00%	20.22%	NA
Indica III	913	56.50%	0.50%	0.11%	42.83%	NA
Indica Intermediate	786	78.60%	3.20%	0.13%	18.07%	NA
Temperate Japonica	767	84.90%	0.00%	0.13%	14.99%	NA
Tropical Japonica	504	81.00%	0.00%	0.00%	19.05%	NA
Japonica Intermediate	241	55.60%	2.10%	0.41%	41.91%	NA
VI/Aromatic	96	64.60%	20.80%	1.04%	13.54%	NA
Intermediate	90	80.00%	11.10%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009470579	T -> A	LOC_Os10g18660.1	upstream_gene_variant ; 1708.0bp to feature; MODIFIER	silent_mutation	Average:14.555; most accessible tissue: Callus, score: 27.709	N	N	N	N
vg1009470579	T -> A	LOC_Os10g18660-LOC_Os10g18670	intergenic_region ; MODIFIER	silent_mutation	Average:14.555; most accessible tissue: Callus, score: 27.709	N	N	N	N
vg1009470579	T -> DEL	N	N	silent_mutation	Average:14.555; most accessible tissue: Callus, score: 27.709	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009470579	NA	2.25E-06	mr1126	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
vg1009470579	NA	2.95E-15	mr1409	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
vg1009470579	NA	1.05E-09	mr1585	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
vg1009470579	8.99E-09	NA	mr1024_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
vg1009470579	NA	1.34E-11	mr1409_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
vg1009470579	9.20E-07	4.23E-08	mr1559_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
vg1009470579	NA	4.75E-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