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Detailed information for vg1001367351:

Variant ID: vg1001367351 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1367351
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

GCGATTTTGCTAGATATCAGTACCACAGTGTTTTTTTTCTCTTTCTTTTTAGGCCTTGTTTAGTTTCCAAAACAAAAACTTTTCACCCATCACATCGAAT[G/A]
TTTGGACACATGCATAGAGTATTAATTAAGGAGGAAAAAAAACATTTACATAGTTTGCGTGTAAATTGCGAGATGAATCTTTTAAACCTAATTGCGTCAT

Reverse complement sequence

ATGACGCAATTAGGTTTAAAAGATTCATCTCGCAATTTACACGCAAACTATGTAAATGTTTTTTTTCCTCCTTAATTAATACTCTATGCATGTGTCCAAA[C/T]
ATTCGATGTGATGGGTGAAAAGTTTTTGTTTTGGAAACTAAACAAGGCCTAAAAAGAAAGAGAAAAAAAACACTGTGGTACTGATATCTAGCAAAATCGC

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	74.30%	22.00%	0.59%	3.07%	NA
All Indica	2759	64.90%	29.30%	0.87%	4.97%	NA
All Japonica	1512	94.90%	4.80%	0.13%	0.13%	NA
Aus	269	46.10%	53.90%	0.00%	0.00%	NA
Indica I	595	62.40%	37.30%	0.34%	0.00%	NA
Indica II	465	68.20%	29.00%	0.43%	2.37%	NA
Indica III	913	64.50%	23.50%	1.31%	10.62%	NA
Indica Intermediate	786	65.30%	30.00%	1.02%	3.69%	NA
Temperate Japonica	767	99.70%	0.10%	0.00%	0.13%	NA
Tropical Japonica	504	86.10%	13.70%	0.00%	0.20%	NA
Japonica Intermediate	241	97.90%	1.20%	0.83%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	76.70%	14.40%	2.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001367351	G -> A	LOC_Os10g03250.1	upstream_gene_variant ; 4936.0bp to feature; MODIFIER	silent_mutation	Average:66.671; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N
vg1001367351	G -> A	LOC_Os10g03240.1	intron_variant ; MODIFIER	silent_mutation	Average:66.671; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N
vg1001367351	G -> DEL	N	N	silent_mutation	Average:66.671; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001367351	9.69E-06	NA	mr1486	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
vg1001367351	6.99E-09	2.33E-12	mr1486	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
vg1001367351	1.09E-07	1.92E-09	mr1548	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
vg1001367351	NA	4.77E-06	mr1588	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
vg1001367351	NA	1.94E-07	mr1721	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
vg1001367351	9.55E-07	2.61E-10	mr1486_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
vg1001367351	3.10E-09	NA	mr1721_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
vg1001367351	3.94E-09	1.71E-11	mr1721_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