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Detailed information for vg1009290760:

Variant ID: vg1009290760 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9290760
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAACTTAATTAAAAACTTTCAACTGAAATTAAAGGTGATAGATTCAATTTCTAAAATTAAAAAAAGGCAAAATTTGCAACAGGACACTGAAATATTGTG[G/T]
CCTTTGCTGTGAGACACCCAAAAATCGTGAATCTTTTCGAGAACACTGTAAAAAAGTGGTAATTAGCTACTGGACACTACTCACATTATTTTATTATTTT

Reverse complement sequence

AAAATAATAAAATAATGTGAGTAGTGTCCAGTAGCTAATTACCACTTTTTTACAGTGTTCTCGAAAAGATTCACGATTTTTGGGTGTCTCACAGCAAAGG[C/A]
CACAATATTTCAGTGTCCTGTTGCAAATTTTGCCTTTTTTTAATTTTAGAAATTGAATCTATCACCTTTAATTTCAGTTGAAAGTTTTTAATTAAGTTAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.10%	4.60%	0.06%	5.27%	NA
All Indica	2759	98.70%	0.80%	0.00%	0.51%	NA
All Japonica	1512	76.60%	8.20%	0.20%	15.01%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	97.50%	1.30%	0.00%	1.20%	NA
Indica Intermediate	786	98.60%	1.10%	0.00%	0.25%	NA
Temperate Japonica	767	94.30%	0.30%	0.13%	5.35%	NA
Tropical Japonica	504	45.60%	20.80%	0.40%	33.13%	NA
Japonica Intermediate	241	85.10%	7.10%	0.00%	7.88%	NA
VI/Aromatic	96	36.50%	61.50%	0.00%	2.08%	NA
Intermediate	90	80.00%	13.30%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009290760	G -> T	LOC_Os10g18294.1	downstream_gene_variant ; 4997.0bp to feature; MODIFIER	silent_mutation	Average:35.324; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg1009290760	G -> T	LOC_Os10g18260-LOC_Os10g18294	intergenic_region ; MODIFIER	silent_mutation	Average:35.324; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg1009290760	G -> DEL	N	N	silent_mutation	Average:35.324; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009290760	NA	6.93E-06	mr1346	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
vg1009290760	NA	3.12E-12	mr1570	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
vg1009290760	NA	3.13E-07	mr1642	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
vg1009290760	4.90E-06	4.91E-06	mr1994	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