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Detailed information for vg1124998850:

Variant ID: vg1124998850 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24998850
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.07, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GACCCCGGCCTTCATCAAACATGGATTTTATGGTTGCTTTTGCCTCGTTGGTGCCTAGCAACGGTGCATCCGGTTCCCATCCATTTTAGACGTGTTAATA[G/A]
TATAGTGACCTGGCCTTGTCGGCACTCGGCCATGGTTTCGTCTAGCCTCGTCGGTCATAGACAAATGAAATGAATGAATAGCTGTAGCCTTGTTAGCTTT

Reverse complement sequence

AAAGCTAACAAGGCTACAGCTATTCATTCATTTCATTTGTCTATGACCGACGAGGCTAGACGAAACCATGGCCGAGTGCCGACAAGGCCAGGTCACTATA[C/T]
TATTAACACGTCTAAAATGGATGGGAACCGGATGCACCGTTGCTAGGCACCAACGAGGCAAAAGCAACCATAAAATCCATGTTTGATGAAGGCCGGGGTC

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	66.20%	33.70%	0.11%	0.00%	NA
All Indica	2759	52.20%	47.60%	0.14%	0.00%	NA
All Japonica	1512	88.20%	11.80%	0.00%	0.00%	NA
Aus	269	86.20%	13.80%	0.00%	0.00%	NA
Indica I	595	38.50%	61.30%	0.17%	0.00%	NA
Indica II	465	59.10%	40.90%	0.00%	0.00%	NA
Indica III	913	57.00%	42.80%	0.22%	0.00%	NA
Indica Intermediate	786	53.10%	46.80%	0.13%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	71.40%	28.60%	0.00%	0.00%	NA
Japonica Intermediate	241	88.40%	11.60%	0.00%	0.00%	NA
VI/Aromatic	96	64.60%	34.40%	1.04%	0.00%	NA
Intermediate	90	66.70%	33.30%	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
vg1124998850	G -> A	LOC_Os11g41650-LOC_Os11g41670	intergenic_region ; MODIFIER	silent_mutation	Average:50.004; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124998850	1.35E-07	NA	mr1191	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
vg1124998850	5.04E-10	5.39E-13	mr1191	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
vg1124998850	5.87E-08	NA	mr1644	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
vg1124998850	1.47E-10	5.02E-14	mr1644	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
vg1124998850	1.32E-07	NA	mr1191_2	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
vg1124998850	2.82E-09	2.34E-15	mr1191_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