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Detailed information for vg1208276198:

Variant ID: vg1208276198 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8276198
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:

ATACATGCAACATGAATTCGTGATCATGGGTCTATTTGCTATGCTTAAAGACTGGACTATTTATTATTCCCCATAAGGGTTATCAACCGAATACTTGTGC[C/T]
AGTCGGGACTCAATTATTATATCTATTTTGGAGTATCCCATAAGGGATAATCACTCAGATCAGAAGCTATTCATATGAGCTATATTTGGTCTATATCACC

Reverse complement sequence

GGTGATATAGACCAAATATAGCTCATATGAATAGCTTCTGATCTGAGTGATTATCCCTTATGGGATACTCCAAAATAGATATAATAATTGAGTCCCGACT[G/A]
GCACAAGTATTCGGTTGATAACCCTTATGGGGAATAATAAATAGTCCAGTCTTTAAGCATAGCAAATAGACCCATGATCACGAATTCATGTTGCATGTAT

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	27.00%	19.20%	0.70%	53.11%	NA
All Indica	2759	44.40%	6.40%	0.43%	48.75%	NA
All Japonica	1512	1.70%	42.40%	0.60%	55.36%	NA
Aus	269	2.60%	13.80%	3.35%	80.30%	NA
Indica I	595	30.10%	8.10%	1.01%	60.84%	NA
Indica II	465	38.30%	7.50%	0.43%	53.76%	NA
Indica III	913	57.90%	2.00%	0.11%	39.98%	NA
Indica Intermediate	786	43.30%	9.50%	0.38%	46.82%	NA
Temperate Japonica	767	0.70%	67.00%	0.26%	32.07%	NA
Tropical Japonica	504	4.00%	11.50%	0.99%	83.53%	NA
Japonica Intermediate	241	0.00%	28.60%	0.83%	70.54%	NA
VI/Aromatic	96	2.10%	20.80%	0.00%	77.08%	NA
Intermediate	90	18.90%	35.60%	3.33%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208276198	C -> DEL	N	N	silent_mutation	Average:26.635; most accessible tissue: Minghui63 flag leaf, score: 58.568	N	N	N	N
vg1208276198	C -> T	LOC_Os12g14500.1	upstream_gene_variant ; 2075.0bp to feature; MODIFIER	silent_mutation	Average:26.635; most accessible tissue: Minghui63 flag leaf, score: 58.568	N	N	N	N
vg1208276198	C -> T	LOC_Os12g14490.1	downstream_gene_variant ; 2092.0bp to feature; MODIFIER	silent_mutation	Average:26.635; most accessible tissue: Minghui63 flag leaf, score: 58.568	N	N	N	N
vg1208276198	C -> T	LOC_Os12g14490-LOC_Os12g14500	intergenic_region ; MODIFIER	silent_mutation	Average:26.635; most accessible tissue: Minghui63 flag leaf, score: 58.568	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208276198	3.60E-06	NA	mr1338_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