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Detailed information for vg1107484286:

Variant ID: vg1107484286 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7484286
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

GGCAAAACTAAAATAAGAATTTCAAAAAAACCAAAATCCAGAAAGCCTACCCAATCCAACCATGCCGCCGCTGTACTCTTGCCGTCGTCGTCACCATGAA[T/C]
ATTGCCATAGACTCAAGCAAGCTCCTCTGCCTCCCTCGTCGGAGTGGAGGGACTAGTCTTTGCTGCCCAATAACGTGTTGTTGGCCGTCATCGTCGCAGT

Reverse complement sequence

ACTGCGACGATGACGGCCAACAACACGTTATTGGGCAGCAAAGACTAGTCCCTCCACTCCGACGAGGGAGGCAGAGGAGCTTGCTTGAGTCTATGGCAAT[A/G]
TTCATGGTGACGACGACGGCAAGAGTACAGCGGCGGCATGGTTGGATTGGGTAGGCTTTCTGGATTTTGGTTTTTTTGAAATTCTTATTTTAGTTTTGCC

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	87.60%	12.40%	0.00%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.00%	0.00%	NA
All Japonica	1512	67.60%	32.40%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	1.00%	0.00%	0.00%	NA
Temperate Japonica	767	66.40%	33.60%	0.00%	0.00%	NA
Tropical Japonica	504	74.20%	25.80%	0.00%	0.00%	NA
Japonica Intermediate	241	57.70%	42.30%	0.00%	0.00%	NA
VI/Aromatic	96	30.20%	69.80%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	0.00%	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
vg1107484286	T -> C	LOC_Os11g13660.1	upstream_gene_variant ; 2498.0bp to feature; MODIFIER	silent_mutation	Average:46.511; most accessible tissue: Callus, score: 58.6	N	N	N	N
vg1107484286	T -> C	LOC_Os11g13650-LOC_Os11g13660	intergenic_region ; MODIFIER	silent_mutation	Average:46.511; most accessible tissue: Callus, score: 58.6	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107484286	6.41E-06	NA	mr1961	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
vg1107484286	NA	1.09E-07	mr1961	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