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Detailed information for vg1123693924:

Variant ID: vg1123693924 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23693924
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.15, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

ATATTTTTTTCACACTTAGGAACTCACAAGAACTAACCATATAAAAAATAAACTCAAACGGACGAAATATGTGGCCTGTGAAATTTTCCAAAGCTCTACC[G/A]
AAAAACTTCTCTCCTCGAAAACACAATCTTGCAAGCGGAATTTGGAGGTTCTAATATCGCCGAACCCGGCAAAGCAGGGAGAATTGGATGTAACTTTTTC

Reverse complement sequence

GAAAAAGTTACATCCAATTCTCCCTGCTTTGCCGGGTTCGGCGATATTAGAACCTCCAAATTCCGCTTGCAAGATTGTGTTTTCGAGGAGAGAAGTTTTT[C/T]
GGTAGAGCTTTGGAAAATTTCACAGGCCACATATTTCGTCCGTTTGAGTTTATTTTTTATATGGTTAGTTCTTGTGAGTTCCTAAGTGTGAAAAAAATAT

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	88.00%	1.00%	10.73%	0.25%	NA
All Indica	2759	85.70%	1.30%	12.58%	0.36%	NA
All Japonica	1512	92.50%	0.50%	6.94%	0.07%	NA
Aus	269	85.50%	0.70%	13.75%	0.00%	NA
Indica I	595	58.20%	4.50%	37.14%	0.17%	NA
Indica II	465	88.20%	0.20%	9.89%	1.72%	NA
Indica III	913	98.10%	0.20%	1.64%	0.00%	NA
Indica Intermediate	786	90.70%	0.90%	8.27%	0.13%	NA
Temperate Japonica	767	93.40%	0.30%	6.26%	0.13%	NA
Tropical Japonica	504	90.30%	1.00%	8.73%	0.00%	NA
Japonica Intermediate	241	94.20%	0.40%	5.39%	0.00%	NA
VI/Aromatic	96	91.70%	0.00%	8.33%	0.00%	NA
Intermediate	90	85.60%	2.20%	11.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123693924	G -> A	LOC_Os11g39740-LOC_Os11g39750	intergenic_region ; MODIFIER	silent_mutation	Average:19.17; most accessible tissue: Zhenshan97 flower, score: 36.732	N	N	N	N
vg1123693924	G -> DEL	N	N	silent_mutation	Average:19.17; most accessible tissue: Zhenshan97 flower, score: 36.732	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123693924	4.44E-06	NA	mr1893_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