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Detailed information for vg1003717312:

Variant ID: vg1003717312 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3717312
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTCTGCCACCAGCTTAAGCTGACAGCTGAGAATTGAAGAGCTACATCAAAGAAATTGTAGATTGTCTAGAAGAATCAAAGAGGTTCTATGTCATTCGT[A/G]
TGAACAGAACATTCATGGAGCAGGACAGAGTGGTAATTTTTCACGCAACATCTCCATCTCCTTATATCCATACCAAGCATATAACTGTCCCATTTCTTTT

Reverse complement sequence

AAAAGAAATGGGACAGTTATATGCTTGGTATGGATATAAGGAGATGGAGATGTTGCGTGAAAAATTACCACTCTGTCCTGCTCCATGAATGTTCTGTTCA[T/C]
ACGAATGACATAGAACCTCTTTGATTCTTCTAGACAATCTACAATTTCTTTGATGTAGCTCTTCAATTCTCAGCTGTCAGCTTAAGCTGGTGGCAGAAGG

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	66.70%	11.10%	0.95%	21.31%	NA
All Indica	2759	49.70%	12.50%	1.59%	36.14%	NA
All Japonica	1512	99.70%	0.10%	0.07%	0.13%	NA
Aus	269	39.40%	60.60%	0.00%	0.00%	NA
Indica I	595	36.50%	30.90%	1.51%	31.09%	NA
Indica II	465	66.20%	1.10%	1.51%	31.18%	NA
Indica III	913	43.90%	7.20%	1.10%	47.75%	NA
Indica Intermediate	786	56.70%	11.60%	2.29%	29.39%	NA
Temperate Japonica	767	99.60%	0.10%	0.13%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	12.20%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003717312	A -> G	LOC_Os10g07060.1	downstream_gene_variant ; 63.0bp to feature; MODIFIER	silent_mutation	Average:13.983; most accessible tissue: Callus, score: 76.93	N	N	N	N
vg1003717312	A -> G	LOC_Os10g07060-LOC_Os10g07080	intergenic_region ; MODIFIER	silent_mutation	Average:13.983; most accessible tissue: Callus, score: 76.93	N	N	N	N
vg1003717312	A -> DEL	N	N	silent_mutation	Average:13.983; most accessible tissue: Callus, score: 76.93	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003717312	NA	7.12E-07	mr1006	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
vg1003717312	NA	5.11E-07	mr1052	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
vg1003717312	2.28E-06	1.56E-09	mr1538_2	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
vg1003717312	NA	1.82E-07	mr1547_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
vg1003717312	NA	2.70E-09	mr1709_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
vg1003717312	NA	8.09E-18	mr1874_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