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Detailed information for vg0906784569:

Variant ID: vg0906784569 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6784569
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTTTTGATGTTAGTCAACTCATGCAAAGGGCTTTGGCTCAAGAAAGTCGGGTTAAGGATAATAGAAAACTTGCTAGACCATTTGACAAAAAGCCTAAT[G/T]
TTAATGTGGTTGATTACCCTGAGGCTAGTGATAGTGAGGAAGAGGGTGATCATGATATTTATGTTGCTGAATGGTCATGGACTAACAAAAATAAGCCTTT

Reverse complement sequence

AAAGGCTTATTTTTGTTAGTCCATGACCATTCAGCAACATAAATATCATGATCACCCTCTTCCTCACTATCACTAGCCTCAGGGTAATCAACCACATTAA[C/A]
ATTAGGCTTTTTGTCAAATGGTCTAGCAAGTTTTCTATTATCCTTAACCCGACTTTCTTGAGCCAAAGCCCTTTGCATGAGTTGACTAACATCAAAAAAT

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	79.60%	18.90%	1.42%	0.00%	NA
All Indica	2759	97.90%	1.90%	0.25%	0.00%	NA
All Japonica	1512	44.40%	52.60%	2.98%	0.00%	NA
Aus	269	95.90%	4.10%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	93.50%	6.00%	0.43%	0.00%	NA
Indica III	913	98.80%	0.90%	0.33%	0.00%	NA
Indica Intermediate	786	98.00%	1.80%	0.25%	0.00%	NA
Temperate Japonica	767	58.50%	38.10%	3.39%	0.00%	NA
Tropical Japonica	504	17.10%	80.00%	2.98%	0.00%	NA
Japonica Intermediate	241	56.40%	41.90%	1.66%	0.00%	NA
VI/Aromatic	96	70.80%	21.90%	7.29%	0.00%	NA
Intermediate	90	74.40%	16.70%	8.89%	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
vg0906784569	G -> T	LOC_Os09g12020-LOC_Os09g12050	intergenic_region ; MODIFIER	silent_mutation	Average:19.179; most accessible tissue: Callus, score: 26.389	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906784569	3.65E-06	4.50E-07	mr1855_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