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Detailed information for vg1119761118:

Variant ID: vg1119761118 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19761118
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAATATCCAAGCGAATTCGCACAGTGAATTTTATCCTAACTAAACCATATAACAGTAATATGATTAAAATAGCATTCACCCATTGCAACGCACGGGCA[G/A]
TTTTTCTAGTAAATAGATTAAAAATCAAACTAACTCAATCATCGAGCTATACACCAACCAAGGAATTCTTGATGGCATATCAATCTACGACTACTATTAC

Reverse complement sequence

GTAATAGTAGTCGTAGATTGATATGCCATCAAGAATTCCTTGGTTGGTGTATAGCTCGATGATTGAGTTAGTTTGATTTTTAATCTATTTACTAGAAAAA[C/T]
TGCCCGTGCGTTGCAATGGGTGAATGCTATTTTAATCATATTACTGTTATATGGTTTAGTTAGGATAAAATTCACTGTGCGAATTCGCTTGGATATTTTT

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	48.30%	20.80%	0.53%	30.32%	NA
All Indica	2759	54.20%	33.50%	0.29%	12.07%	NA
All Japonica	1512	29.80%	2.40%	0.99%	66.73%	NA
Aus	269	95.90%	0.40%	0.00%	3.72%	NA
Indica I	595	60.20%	38.50%	0.00%	1.34%	NA
Indica II	465	70.50%	25.40%	0.00%	4.09%	NA
Indica III	913	42.70%	34.80%	0.44%	22.02%	NA
Indica Intermediate	786	53.30%	32.80%	0.51%	13.36%	NA
Temperate Japonica	767	45.20%	3.00%	0.65%	51.11%	NA
Tropical Japonica	504	8.70%	2.60%	1.39%	87.30%	NA
Japonica Intermediate	241	24.90%	0.40%	1.24%	73.44%	NA
VI/Aromatic	96	32.30%	2.10%	1.04%	64.58%	NA
Intermediate	90	53.30%	24.40%	1.11%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119761118	G -> A	LOC_Os11g33394.1	intron_variant ; MODIFIER	silent_mutation	Average:36.539; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1119761118	G -> A	LOC_Os11g33394.2	intron_variant ; MODIFIER	silent_mutation	Average:36.539; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1119761118	G -> DEL	N	N	silent_mutation	Average:36.539; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119761118	NA	3.91E-06	mr1910	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
vg1119761118	NA	1.52E-07	mr1092_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
vg1119761118	NA	7.90E-06	mr1097_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
vg1119761118	NA	6.96E-09	mr1152_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
vg1119761118	NA	4.42E-09	mr1154_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
vg1119761118	NA	2.74E-06	mr1389_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