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Detailed information for vg1219066039:

Variant ID: vg1219066039 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19066039
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:

GTCTACATCACCGTTGGGCAGAAAATAGACATAACACATAGAGCCATAACTATAACATTGCAATTATCAACGTTGGTCAGAAAATTACAACATCATAGCA[C/T]
ATAATTAATGTTCCTAAAATCAAATTCTCCCGTTGGTTCGAAATTTAATTTTAGAAACACTAATTTTCATCAATTTCATCTATTTGCAGTGGAAGATCTA

Reverse complement sequence

TAGATCTTCCACTGCAAATAGATGAAATTGATGAAAATTAGTGTTTCTAAAATTAAATTTCGAACCAACGGGAGAATTTGATTTTAGGAACATTAATTAT[G/A]
TGCTATGATGTTGTAATTTTCTGACCAACGTTGATAATTGCAATGTTATAGTTATGGCTCTATGTGTTATGTCTATTTTCTGCCCAACGGTGATGTAGAC

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	93.00%	6.60%	0.42%	0.00%	NA
All Indica	2759	88.20%	11.10%	0.65%	0.00%	NA
All Japonica	1512	99.60%	0.30%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	86.60%	12.90%	0.50%	0.00%	NA
Indica II	465	89.20%	9.70%	1.08%	0.00%	NA
Indica III	913	88.10%	11.20%	0.77%	0.00%	NA
Indica Intermediate	786	89.10%	10.60%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg1219066039	C -> T	LOC_Os12g31660.1	downstream_gene_variant ; 3712.0bp to feature; MODIFIER	silent_mutation	Average:43.129; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg1219066039	C -> T	LOC_Os12g31650.1	intron_variant ; MODIFIER	silent_mutation	Average:43.129; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219066039	4.55E-06	5.68E-06	mr1588	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