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Detailed information for vg0911115830:

Variant ID: vg0911115830 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11115830
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGAAATAAAACAATAGCTTTAAACGGGTTCAACATGCTCAAAGGGTTGTTTGGGAACTGTGTGACTTGCCTTTGAAACAAGCGTCTTCAATTCGTCTT[T/C]
AGGAACTTCTCCAACGAACGAACGATCCTCCGAAACAACGGAAAACAAAACCTAGAACGCAAAACGAGAAAAAAACACTAATAAAAACCAAATAAACAGT

Reverse complement sequence

ACTGTTTATTTGGTTTTTATTAGTGTTTTTTTCTCGTTTTGCGTTCTAGGTTTTGTTTTCCGTTGTTTCGGAGGATCGTTCGTTCGTTGGAGAAGTTCCT[A/G]
AAGACGAATTGAAGACGCTTGTTTCAAAGGCAAGTCACACAGTTCCCAAACAACCCTTTGAGCATGTTGAACCCGTTTAAAGCTATTGTTTTATTTCAAC

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	35.70%	35.30%	22.96%	6.05%	NA
All Indica	2759	10.10%	57.10%	29.65%	3.19%	NA
All Japonica	1512	86.60%	1.70%	3.44%	8.27%	NA
Aus	269	16.00%	16.70%	46.47%	20.82%	NA
Indica I	595	13.90%	73.10%	10.92%	2.02%	NA
Indica II	465	13.50%	36.80%	41.51%	8.17%	NA
Indica III	913	5.40%	57.50%	36.14%	0.99%	NA
Indica Intermediate	786	10.60%	56.50%	29.26%	3.69%	NA
Temperate Japonica	767	90.10%	0.80%	4.69%	4.43%	NA
Tropical Japonica	504	88.70%	1.60%	0.79%	8.93%	NA
Japonica Intermediate	241	71.40%	4.60%	4.98%	19.09%	NA
VI/Aromatic	96	10.40%	6.20%	69.79%	13.54%	NA
Intermediate	90	52.20%	17.80%	25.56%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911115830	T -> DEL	N	N	silent_mutation	Average:18.283; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0911115830	T -> C	LOC_Os09g18130-LOC_Os09g18159	intergenic_region ; MODIFIER	silent_mutation	Average:18.283; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911115830	9.82E-07	9.82E-07	mr1973_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