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Detailed information for vg0811720061:

Variant ID: vg0811720061 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 11720061
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

CGATCCAAGTTATTCACCTTCATTTAATTGGGATCTTTACATTTGAACATATATTTGAGTATATGACACTTGTGGTGTTGATTAATACTCATCATTTATT[C/T]
ATATCCTTTTATACATGCGATCGGTTGGTCAACATATGGAGGTTGACAACCGGATCATTGGGACTAATAATTTTATTGAGTTAAATGAAAGAAATAGGTC

Reverse complement sequence

GACCTATTTCTTTCATTTAACTCAATAAAATTATTAGTCCCAATGATCCGGTTGTCAACCTCCATATGTTGACCAACCGATCGCATGTATAAAAGGATAT[G/A]
AATAAATGATGAGTATTAATCAACACCACAAGTGTCATATACTCAAATATATGTTCAAATGTAAAGATCCCAATTAAATGAAGGTGAATAACTTGGATCG

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	84.10%	8.80%	5.82%	1.31%	NA
All Indica	2759	94.40%	0.30%	5.07%	0.22%	NA
All Japonica	1512	66.70%	22.50%	7.67%	3.11%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	98.30%	0.20%	1.34%	0.17%	NA
Indica II	465	96.60%	0.20%	3.01%	0.22%	NA
Indica III	913	90.30%	0.20%	9.09%	0.44%	NA
Indica Intermediate	786	95.00%	0.50%	4.45%	0.00%	NA
Temperate Japonica	767	84.90%	3.10%	10.30%	1.69%	NA
Tropical Japonica	504	47.80%	41.90%	4.56%	5.75%	NA
Japonica Intermediate	241	48.50%	43.60%	5.81%	2.07%	NA
VI/Aromatic	96	20.80%	55.20%	16.67%	7.29%	NA
Intermediate	90	81.10%	14.40%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0811720061	C -> T	LOC_Os08g19600.1	upstream_gene_variant ; 1439.0bp to feature; MODIFIER	silent_mutation	Average:30.175; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0811720061	C -> T	LOC_Os08g19600-LOC_Os08g19610	intergenic_region ; MODIFIER	silent_mutation	Average:30.175; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0811720061	C -> DEL	N	N	silent_mutation	Average:30.175; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0811720061	8.97E-06	NA	mr1242_2	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
vg0811720061	6.26E-06	NA	mr1496_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