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Detailed information for vg0902628748:

Variant ID: vg0902628748 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 2628748
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.04, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

AAACCGATTTAGTTTGCTTTGATTCTCTAAAAATATAACCGTCGAGTTAGACTTTATTTAAAATTTTATTTTCCATGCTTATTTTTGATGTTTCTTTTCT[C/T]
GTTTAATTTTGTCGCAAAGTGCATATCATCCCTCAAATAATTCCTTTGATCCGATTTAAATCTATCCCGAATGTCGGACTGTCTAAATTCCACATCAATT

Reverse complement sequence

AATTGATGTGGAATTTAGACAGTCCGACATTCGGGATAGATTTAAATCGGATCAAAGGAATTATTTGAGGGATGATATGCACTTTGCGACAAAATTAAAC[G/A]
AGAAAAGAAACATCAAAAATAAGCATGGAAAATAAAATTTTAAATAAAGTCTAACTCGACGGTTATATTTTTAGAGAATCAAAGCAAACTAAATCGGTTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.80%	37.20%	0.00%	0.00%	NA
All Indica	2759	95.90%	4.10%	0.00%	0.00%	NA
All Japonica	1512	1.10%	98.90%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	95.10%	4.90%	0.00%	0.00%	NA
Indica II	465	91.60%	8.40%	0.00%	0.00%	NA
Indica III	913	98.80%	1.20%	0.00%	0.00%	NA
Indica Intermediate	786	95.50%	4.50%	0.00%	0.00%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	5.20%	94.80%	0.00%	0.00%	NA
Intermediate	90	38.90%	61.10%	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
vg0902628748	C -> T	LOC_Os09g04900.1	upstream_gene_variant ; 2097.0bp to feature; MODIFIER	silent_mutation	Average:39.307; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg0902628748	C -> T	LOC_Os09g04910.1	downstream_gene_variant ; 1582.0bp to feature; MODIFIER	silent_mutation	Average:39.307; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg0902628748	C -> T	LOC_Os09g04900-LOC_Os09g04910	intergenic_region ; MODIFIER	silent_mutation	Average:39.307; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0902628748	1.69E-06	NA	mr1542_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