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Detailed information for vg1108092829:

Variant ID: vg1108092829 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8092829
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: 39. )

Flanking Sequence (100 bp) in Reference Genome:

CATAAAATTATATTTAACAATAAATCAAATGATAGGAAAAGAATTAATAATTACTTAAATTTTTTGAATAAGACGAACGGTCAAACATTTTTAAAAAAAT[C/T]
AACGGCGTCAAATATTTTGGGATGGAGTAAGTATAGTAGAAGTGTTATATTAATAAGAGAGTACTTATTTTTTGAATGGGCTGACATTTCTTAGCTGGAC

Reverse complement sequence

GTCCAGCTAAGAAATGTCAGCCCATTCAAAAAATAAGTACTCTCTTATTAATATAACACTTCTACTATACTTACTCCATCCCAAAATATTTGACGCCGTT[G/A]
ATTTTTTTAAAAATGTTTGACCGTTCGTCTTATTCAAAAAATTTAAGTAATTATTAATTCTTTTCCTATCATTTGATTTATTGTTAAATATAATTTTATG

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	37.20%	0.40%	1.69%	60.75%	NA
All Indica	2759	5.00%	0.10%	0.51%	94.45%	NA
All Japonica	1512	86.30%	0.90%	3.37%	9.46%	NA
Aus	269	71.40%	0.00%	2.97%	25.65%	NA
Indica I	595	7.70%	0.00%	0.67%	91.60%	NA
Indica II	465	1.50%	0.00%	0.22%	98.28%	NA
Indica III	913	2.00%	0.00%	0.44%	97.59%	NA
Indica Intermediate	786	8.40%	0.30%	0.64%	90.71%	NA
Temperate Japonica	767	92.60%	1.60%	3.91%	1.96%	NA
Tropical Japonica	504	78.60%	0.20%	2.78%	18.45%	NA
Japonica Intermediate	241	82.60%	0.00%	2.90%	14.52%	NA
VI/Aromatic	96	89.60%	0.00%	3.12%	7.29%	NA
Intermediate	90	41.10%	3.30%	4.44%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108092829	C -> T	LOC_Os11g14410.1	upstream_gene_variant ; 606.0bp to feature; MODIFIER	silent_mutation	Average:14.562; most accessible tissue: Callus, score: 28.034	N	N	N	N
vg1108092829	C -> T	LOC_Os11g14420.1	upstream_gene_variant ; 3040.0bp to feature; MODIFIER	silent_mutation	Average:14.562; most accessible tissue: Callus, score: 28.034	N	N	N	N
vg1108092829	C -> T	LOC_Os11g14410-LOC_Os11g14420	intergenic_region ; MODIFIER	silent_mutation	Average:14.562; most accessible tissue: Callus, score: 28.034	N	N	N	N
vg1108092829	C -> DEL	N	N	silent_mutation	Average:14.562; most accessible tissue: Callus, score: 28.034	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108092829	1.29E-06	2.92E-07	mr1388_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