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Detailed information for vg1104839489:

Variant ID: vg1104839489 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4839489
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

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

Flanking Sequence (100 bp) in Reference Genome:

CCATTTTCCCCTAAATTAATGCCATTATGTTGCCTTAACGGAATAGGGTACTCTTCGTCTTTTGAAAAACAGGGTCAAATGGGTAAACTTAAGAAAGTAC[G/A]
GCCAAAATAGTGGTTAGACTTTAAAATATGGCCAAAAGTACAATTGCCCCAAAATCTAACTACTCAAACCTATTGAAAAATTCATATGGATTGATGTTTG

Reverse complement sequence

CAAACATCAATCCATATGAATTTTTCAATAGGTTTGAGTAGTTAGATTTTGGGGCAATTGTACTTTTGGCCATATTTTAAAGTCTAACCACTATTTTGGC[C/T]
GTACTTTCTTAAGTTTACCCATTTGACCCTGTTTTTCAAAAGACGAAGAGTACCCTATTCCGTTAAGGCAACATAATGGCATTAATTTAGGGGAAAATGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.00%	14.00%	0.00%	0.00%	NA
All Indica	2759	80.60%	19.40%	0.00%	0.00%	NA
All Japonica	1512	95.00%	5.00%	0.00%	0.00%	NA
Aus	269	83.60%	16.40%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	96.30%	3.70%	0.00%	0.00%	NA
Indica III	913	55.50%	44.50%	0.00%	0.00%	NA
Indica Intermediate	786	87.50%	12.50%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	87.70%	12.30%	0.00%	0.00%	NA
Japonica Intermediate	241	94.60%	5.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg1104839489	G -> A	LOC_Os11g09100-LOC_Os11g09110	intergenic_region ; MODIFIER	silent_mutation	Average:27.132; most accessible tissue: Callus, score: 68.705	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104839489	2.51E-06	2.51E-06	mr1513	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
vg1104839489	NA	8.76E-06	mr1695	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