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Detailed information for vg1018616939:

Variant ID: vg1018616939 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 18616939
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.05, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGTGTACGACAACTGTGCTACCTGCATTTCAATTTGTTAGTATCAAATAAAGTGTTGTGACATGCATTTTTCTATGTTACTTGTTTATTCAAATTACC[G/A]
GTGTAGTATGTGACTTAAGCATGGTTAACTCATCATGTAGTAATGCTGGGCTTTGTGGCGATTGGGTTGTGCCGATTCCTGTGAATTGAAAAGCATGATG

Reverse complement sequence

CATCATGCTTTTCAATTCACAGGAATCGGCACAACCCAATCGCCACAAAGCCCAGCATTACTACATGATGAGTTAACCATGCTTAAGTCACATACTACAC[C/T]
GGTAATTTGAATAAACAAGTAACATAGAAAAATGCATGTCACAACACTTTATTTGATACTAACAAATTGAAATGCAGGTAGCACAGTTGTCGTACACAAG

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	45.40%	31.50%	2.48%	20.59%	NA
All Indica	2759	73.00%	3.40%	2.86%	20.70%	NA
All Japonica	1512	1.70%	87.50%	0.73%	10.05%	NA
Aus	269	24.90%	1.90%	5.95%	67.29%	NA
Indica I	595	81.00%	3.50%	4.20%	11.26%	NA
Indica II	465	74.00%	2.20%	2.15%	21.72%	NA
Indica III	913	72.10%	3.00%	1.42%	23.55%	NA
Indica Intermediate	786	67.40%	4.70%	3.94%	23.92%	NA
Temperate Japonica	767	1.30%	96.20%	0.13%	2.35%	NA
Tropical Japonica	504	2.60%	73.80%	1.79%	21.83%	NA
Japonica Intermediate	241	1.20%	88.40%	0.41%	9.96%	NA
VI/Aromatic	96	3.10%	45.80%	3.12%	47.92%	NA
Intermediate	90	40.00%	25.60%	8.89%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1018616939	G -> A	LOC_Os10g34884.1	missense_variant&splice_region_variant ; p.Pro261Leu; MODERATE	nonsynonymous_codon ; P261L	Average:34.205; most accessible tissue: Callus, score: 61.326	unknown	unknown	TOLERATED	0.31
vg1018616939	G -> DEL	LOC_Os10g34884.1	N	frameshift_variant	Average:34.205; most accessible tissue: Callus, score: 61.326	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1018616939	NA	6.48E-17	mr1484	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
vg1018616939	NA	1.23E-38	mr1784	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
vg1018616939	NA	5.73E-14	mr1909	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
vg1018616939	7.82E-07	1.10E-06	mr1925	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
vg1018616939	NA	1.41E-10	mr1945	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
vg1018616939	NA	1.04E-12	mr1217_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
vg1018616939	NA	6.86E-52	mr1261_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
vg1018616939	NA	1.78E-06	mr1275_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
vg1018616939	NA	4.51E-14	mr1575_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
vg1018616939	NA	7.00E-12	mr1641_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
vg1018616939	NA	2.34E-25	mr1653_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
vg1018616939	NA	1.63E-10	mr1667_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
vg1018616939	NA	8.22E-11	mr1714_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
vg1018616939	NA	1.02E-19	mr1731_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
vg1018616939	NA	3.69E-16	mr1767_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
vg1018616939	NA	5.09E-13	mr1838_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
vg1018616939	NA	2.79E-08	mr1909_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
vg1018616939	NA	8.77E-08	mr1921_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