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Detailed information for vg0909789211:

Variant ID: vg0909789211 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9789211
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

TATGGAGAAGATAAAAGAAAAAAAAAGATGAGCAGCGGGTAACAGGTGTGACTATATATTAATAGTGTAGGACTCCCTCCGTTTCACAATGTAAGTCATT[C/T]
TAGCATTTCCTACATTCATATCTAGACATATATATCTATCTAGATTTATTAACATCCATATGAATATGGGAAATGCTAGAATAACTTACATTGTGAAACG

Reverse complement sequence

CGTTTCACAATGTAAGTTATTCTAGCATTTCCCATATTCATATGGATGTTAATAAATCTAGATAGATATATATGTCTAGATATGAATGTAGGAAATGCTA[G/A]
AATGACTTACATTGTGAAACGGAGGGAGTCCTACACTATTAATATATAGTCACACCTGTTACCCGCTGCTCATCTTTTTTTTTCTTTTATCTTCTCCATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.20%	15.10%	0.89%	2.77%	NA
All Indica	2759	78.70%	20.40%	0.65%	0.22%	NA
All Japonica	1512	89.00%	4.40%	1.39%	5.29%	NA
Aus	269	72.90%	26.40%	0.37%	0.37%	NA
Indica I	595	87.60%	12.10%	0.34%	0.00%	NA
Indica II	465	79.80%	19.10%	1.08%	0.00%	NA
Indica III	913	72.30%	26.70%	0.33%	0.66%	NA
Indica Intermediate	786	78.80%	20.20%	1.02%	0.00%	NA
Temperate Japonica	767	93.70%	2.70%	0.13%	3.39%	NA
Tropical Japonica	504	80.40%	7.90%	3.57%	8.13%	NA
Japonica Intermediate	241	91.70%	2.10%	0.83%	5.39%	NA
VI/Aromatic	96	51.00%	10.40%	1.04%	37.50%	NA
Intermediate	90	85.60%	4.40%	1.11%	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
vg0909789211	C -> DEL	N	N	silent_mutation	Average:44.842; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0909789211	C -> T	LOC_Os09g16020.1	downstream_gene_variant ; 3067.0bp to feature; MODIFIER	silent_mutation	Average:44.842; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0909789211	C -> T	LOC_Os09g16030.1	downstream_gene_variant ; 1220.0bp to feature; MODIFIER	silent_mutation	Average:44.842; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0909789211	C -> T	LOC_Os09g16020-LOC_Os09g16030	intergenic_region ; MODIFIER	silent_mutation	Average:44.842; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909789211	4.02E-07	NA	mr1807	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