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Detailed information for vg0527430964:

Variant ID: vg0527430964 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 27430964
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

TTAATGCGTGACTCTCCATTCTTCCACACAGGATTGGCTACATGGGCATCGAGAAATGTAAATATTAATGAATCGCTTGTTTACGAGGAATAACTAGTAG[C/T]
ATATTTAAATGGATGATAAGTAGAATTACTTATCCTTAGTCTGTGTGCTAAAATGAAATATGACTATCAAAAGTATATGGAGGGAGTATTTTGGAACGGA

Reverse complement sequence

TCCGTTCCAAAATACTCCCTCCATATACTTTTGATAGTCATATTTCATTTTAGCACACAGACTAAGGATAAGTAATTCTACTTATCATCCATTTAAATAT[G/A]
CTACTAGTTATTCCTCGTAAACAAGCGATTCATTAATATTTACATTTCTCGATGCCCATGTAGCCAATCCTGTGTGGAAGAATGGAGAGTCACGCATTAA

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	59.70%	40.20%	0.13%	0.00%	NA
All Indica	2759	87.50%	12.40%	0.14%	0.00%	NA
All Japonica	1512	19.50%	80.50%	0.00%	0.00%	NA
Aus	269	13.40%	86.20%	0.37%	0.00%	NA
Indica I	595	94.10%	5.70%	0.17%	0.00%	NA
Indica II	465	63.00%	37.00%	0.00%	0.00%	NA
Indica III	913	96.60%	3.40%	0.00%	0.00%	NA
Indica Intermediate	786	86.40%	13.20%	0.38%	0.00%	NA
Temperate Japonica	767	1.80%	98.20%	0.00%	0.00%	NA
Tropical Japonica	504	51.80%	48.20%	0.00%	0.00%	NA
Japonica Intermediate	241	8.30%	91.70%	0.00%	0.00%	NA
VI/Aromatic	96	37.50%	62.50%	0.00%	0.00%	NA
Intermediate	90	45.60%	53.30%	1.11%	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
vg0527430964	C -> T	LOC_Os05g47840-LOC_Os05g47850	intergenic_region ; MODIFIER	silent_mutation	Average:33.984; most accessible tissue: Callus, score: 57.335	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0527430964	NA	4.07E-06	mr1044	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
vg0527430964	NA	4.92E-10	mr1349_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
vg0527430964	NA	9.22E-06	mr1349_2	Ind_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
vg0527430964	NA	1.31E-07	mr1817_2	Jap_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