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Detailed information for vg1011259905:

Variant ID: vg1011259905 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11259905
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

TGAACTTAATTAATCTTGGGATTAATTTAAGGAAATAACTATATTTATGGCGCTATATTTTTCACTAAAAAATAGTCGGTATGTATTTACAATGTAAGTC[C/T]
CTAAATTACATAAATAGTCGGTATGTATTTACAATGTAAGTCCCTAAATTACATATGTAGTTTTAGTGTATTTACAATGTAAATCCCAAAATTACATATA

Reverse complement sequence

TATATGTAATTTTGGGATTTACATTGTAAATACACTAAAACTACATATGTAATTTAGGGACTTACATTGTAAATACATACCGACTATTTATGTAATTTAG[G/A]
GACTTACATTGTAAATACATACCGACTATTTTTTAGTGAAAAATATAGCGCCATAAATATAGTTATTTCCTTAAATTAATCCCAAGATTAATTAAGTTCA

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	99.50%	0.20%	0.30%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	98.60%	0.50%	0.86%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	98.70%	0.50%	0.78%	0.00%	NA
Tropical Japonica	504	99.00%	0.20%	0.79%	0.00%	NA
Japonica Intermediate	241	97.50%	1.20%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	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
vg1011259905	C -> T	LOC_Os10g21890.1	downstream_gene_variant ; 4316.0bp to feature; MODIFIER	silent_mutation	Average:44.131; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1011259905	C -> T	LOC_Os10g21890.2	downstream_gene_variant ; 4316.0bp to feature; MODIFIER	silent_mutation	Average:44.131; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1011259905	C -> T	LOC_Os10g21890-LOC_Os10g21910	intergenic_region ; MODIFIER	silent_mutation	Average:44.131; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011259905	NA	1.54E-06	mr1617_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
vg1011259905	3.73E-06	9.33E-09	mr1705_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