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Detailed information for vg1001457313:

Variant ID: vg1001457313 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1457313
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.56, A: 0.44, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAATTCTAATGCCACGTAAGCGCTACGTGGGATGAAAACTAGGTCAACATTGCCACGTCAGCGCCACATCAGCAAAACCGCCATCCAAAACCGCCGAG[G/A]
GAGTCAAATTGCACTGGTTTCAATAGTTCGGGGAGTCGTCTTGAGGTTTATGGATTAGATTCGAGTCACTTTTAAGGGAGTTAAAGTGGACTTATTCCTA

Reverse complement sequence

TAGGAATAAGTCCACTTTAACTCCCTTAAAAGTGACTCGAATCTAATCCATAAACCTCAAGACGACTCCCCGAACTATTGAAACCAGTGCAATTTGACTC[C/T]
CTCGGCGGTTTTGGATGGCGGTTTTGCTGATGTGGCGCTGACGTGGCAATGTTGACCTAGTTTTCATCCCACGTAGCGCTTACGTGGCATTAGAATTAAA

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	61.20%	11.60%	0.49%	26.75%	NA
All Indica	2759	76.90%	10.50%	0.33%	12.18%	NA
All Japonica	1512	40.80%	4.80%	0.46%	53.97%	NA
Aus	269	34.20%	62.80%	1.12%	1.86%	NA
Indica I	595	86.10%	1.50%	0.17%	12.27%	NA
Indica II	465	91.00%	2.40%	0.00%	6.67%	NA
Indica III	913	66.80%	18.00%	0.55%	14.68%	NA
Indica Intermediate	786	73.50%	13.60%	0.38%	12.47%	NA
Temperate Japonica	767	71.80%	0.00%	0.39%	27.77%	NA
Tropical Japonica	504	5.20%	13.50%	0.40%	80.95%	NA
Japonica Intermediate	241	16.60%	1.70%	0.83%	80.91%	NA
VI/Aromatic	96	14.60%	5.20%	3.12%	77.08%	NA
Intermediate	90	50.00%	12.20%	1.11%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001457313	G -> A	LOC_Os10g03410.1	downstream_gene_variant ; 3918.0bp to feature; MODIFIER	silent_mutation	Average:62.972; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg1001457313	G -> A	LOC_Os10g03420.1	downstream_gene_variant ; 211.0bp to feature; MODIFIER	silent_mutation	Average:62.972; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg1001457313	G -> A	LOC_Os10g03420-LOC_Os10g03430	intergenic_region ; MODIFIER	silent_mutation	Average:62.972; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg1001457313	G -> DEL	N	N	silent_mutation	Average:62.972; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001457313	2.37E-11	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
vg1001457313	1.84E-11	NA	mr1548	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
vg1001457313	7.41E-07	NA	mr1588	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
vg1001457313	3.21E-13	NA	mr1486_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
vg1001457313	5.92E-13	NA	mr1588_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