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Detailed information for vg1123674215:

Variant ID: vg1123674215 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23674215
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.71, G: 0.30, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

AGATAACCTCTCTTGAAAGGATTCAAATTCAGGTCGGTGCACAGTGCAGTGTTGTGGAAGACGGTATACGGATATCGGACGGAGAGAGTACCGCTAAACG[G/A]
TTAATCGGAATGCGGACGATTAATCGGAATTTGGCGGAAATATAACGTTTTGAAAGTATATGTACATAGTTGATAATAGTTTTCCCTTTTTGATAAACAA

Reverse complement sequence

TTGTTTATCAAAAAGGGAAAACTATTATCAACTATGTACATATACTTTCAAAACGTTATATTTCCGCCAAATTCCGATTAATCGTCCGCATTCCGATTAA[C/T]
CGTTTAGCGGTACTCTCTCCGTCCGATATCCGTATACCGTCTTCCACAACACTGCACTGTGCACCGACCTGAATTTGAATCCTTTCAAGAGAGGTTATCT

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	46.40%	44.60%	1.76%	7.24%	NA
All Indica	2759	32.10%	55.20%	2.03%	10.69%	NA
All Japonica	1512	68.50%	29.80%	0.73%	1.06%	NA
Aus	269	69.90%	23.80%	3.72%	2.60%	NA
Indica I	595	20.80%	73.10%	1.01%	5.04%	NA
Indica II	465	11.00%	64.90%	1.94%	22.15%	NA
Indica III	913	50.30%	36.40%	2.74%	10.62%	NA
Indica Intermediate	786	31.90%	57.80%	2.04%	8.27%	NA
Temperate Japonica	767	77.60%	20.20%	0.52%	1.69%	NA
Tropical Japonica	504	49.60%	49.20%	1.19%	0.00%	NA
Japonica Intermediate	241	78.80%	19.50%	0.41%	1.24%	NA
VI/Aromatic	96	54.20%	28.10%	2.08%	15.62%	NA
Intermediate	90	38.90%	46.70%	4.44%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123674215	G -> A	LOC_Os11g39730.1	downstream_gene_variant ; 1364.0bp to feature; MODIFIER	silent_mutation	Average:20.349; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1123674215	G -> A	LOC_Os11g39720-LOC_Os11g39730	intergenic_region ; MODIFIER	silent_mutation	Average:20.349; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1123674215	G -> DEL	N	N	silent_mutation	Average:20.349; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123674215	4.10E-07	1.03E-06	mr1528_2	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