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Detailed information for vg1124469615:

Variant ID: vg1124469615 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24469615
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

CCTCCCCCTCCGCGGTAGCACGGGCCAGCTCCCGCCGCCGGTTGCCGCCTTGCCTCGTCGCGCCGCCGCCTAGGGTTTGCAAATAGGGAGCGGCGCGAGG[G/A]
AGCCGAGCTATGGAGGGATGGGTCACGGAGGGAGAGCGAGAGGGCGCCGTCTGGTAGAGTGGTGGCTAAGTGGGTCAACTGATGTCTGATGGGTCACGAC

Reverse complement sequence

GTCGTGACCCATCAGACATCAGTTGACCCACTTAGCCACCACTCTACCAGACGGCGCCCTCTCGCTCTCCCTCCGTGACCCATCCCTCCATAGCTCGGCT[C/T]
CCTCGCGCCGCTCCCTATTTGCAAACCCTAGGCGGCGGCGCGACGAGGCAAGGCGGCAACCGGCGGCGGGAGCTGGCCCGTGCTACCGCGGAGGGGGAGG

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	27.50%	22.70%	1.29%	48.58%	NA
All Indica	2759	38.60%	7.10%	1.12%	53.14%	NA
All Japonica	1512	4.40%	46.20%	1.06%	48.35%	NA
Aus	269	42.00%	30.90%	2.60%	24.54%	NA
Indica I	595	40.30%	3.70%	0.17%	55.80%	NA
Indica II	465	54.20%	13.80%	1.08%	30.97%	NA
Indica III	913	33.30%	4.80%	1.31%	60.57%	NA
Indica Intermediate	786	34.40%	8.40%	1.65%	55.60%	NA
Temperate Japonica	767	3.70%	47.10%	1.04%	48.24%	NA
Tropical Japonica	504	5.20%	50.20%	0.40%	44.25%	NA
Japonica Intermediate	241	5.00%	35.30%	2.49%	57.26%	NA
VI/Aromatic	96	18.80%	67.70%	4.17%	9.38%	NA
Intermediate	90	38.90%	31.10%	3.33%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124469615	G -> A	LOC_Os11g40870-LOC_Os11g40890	intergenic_region ; MODIFIER	silent_mutation	Average:9.179; most accessible tissue: Callus, score: 27.678	N	N	N	N
vg1124469615	G -> DEL	N	N	silent_mutation	Average:9.179; most accessible tissue: Callus, score: 27.678	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124469615	2.15E-11	8.04E-14	mr1238	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
vg1124469615	3.61E-06	NA	mr1309	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
vg1124469615	1.62E-11	3.46E-14	mr1309	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
vg1124469615	6.04E-07	3.00E-08	mr1484	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
vg1124469615	7.44E-06	NA	mr1841	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
vg1124469615	2.52E-08	2.74E-10	mr1841	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
vg1124469615	9.43E-07	9.43E-07	mr1900	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
vg1124469615	2.85E-06	NA	mr1238_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
vg1124469615	4.85E-09	9.70E-13	mr1238_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
vg1124469615	NA	7.07E-06	mr1379_2	Jap_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
vg1124469615	NA	4.31E-06	mr1409_2	Jap_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
vg1124469615	2.10E-06	NA	mr1484_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
vg1124469615	5.21E-10	2.64E-13	mr1484_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
vg1124469615	4.24E-06	NA	mr1609_2	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
vg1124469615	3.16E-06	3.12E-08	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
vg1124469615	7.61E-12	9.82E-17	mr1841_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
vg1124469615	6.91E-09	2.59E-12	mr1900_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
vg1124469615	2.41E-06	NA	mr1945_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
vg1124469615	1.91E-08	1.91E-08	mr1945_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