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Detailed information for vg1124407763:

Variant ID: vg1124407763 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24407763
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

ATCAAATTTTAAAGATTAGCCACTGCCAAATGATACTCTGCTGCACACAACTACAGGGCTGGCTAACGGGCGATTGATCGCTCGATCCCCATCCACCCAT[G/A]
TACACTCCTCTCCCCCCATCCTCCTCTTCTTCTCTTCCTACTACACCATAAATTTTAAAAAAATAAAAAAACAAAGTTAGAAAAATTTATGTATAGAAAT

Reverse complement sequence

ATTTCTATACATAAATTTTTCTAACTTTGTTTTTTTATTTTTTTAAAATTTATGGTGTAGTAGGAAGAGAAGAAGAGGAGGATGGGGGGAGAGGAGTGTA[C/T]
ATGGGTGGATGGGGATCGAGCGATCAATCGCCCGTTAGCCAGCCCTGTAGTTGTGTGCAGCAGAGTATCATTTGGCAGTGGCTAATCTTTAAAATTTGAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.10%	31.50%	0.23%	0.13%	NA
All Indica	2759	59.40%	40.20%	0.18%	0.18%	NA
All Japonica	1512	77.80%	22.00%	0.20%	0.00%	NA
Aus	269	96.70%	2.60%	0.37%	0.37%	NA
Indica I	595	38.30%	61.30%	0.17%	0.17%	NA
Indica II	465	51.40%	48.40%	0.22%	0.00%	NA
Indica III	913	74.50%	25.10%	0.11%	0.33%	NA
Indica Intermediate	786	62.60%	37.00%	0.25%	0.13%	NA
Temperate Japonica	767	61.80%	38.10%	0.13%	0.00%	NA
Tropical Japonica	504	96.40%	3.20%	0.40%	0.00%	NA
Japonica Intermediate	241	89.60%	10.40%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	62.20%	35.60%	2.22%	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
vg1124407763	G -> A	LOC_Os11g40790-LOC_Os11g40800	intergenic_region ; MODIFIER	silent_mutation	Average:51.456; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg1124407763	G -> DEL	N	N	silent_mutation	Average:51.456; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124407763	6.66E-06	3.84E-07	mr1363	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
vg1124407763	NA	4.41E-06	mr1609_2	Ind_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