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Detailed information for vg1002857039:

Variant ID: vg1002857039 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2857039
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTCGGATTGCACTGTATGGGTTCCAATGCTTTTCTAGCAGTACTCCCTCCGGTTTAATTAACGTTTTAGATAAGGTTGAAGTCAAACTTTTATAACTTA[G/A]
ACTATCAATAACTTTAAAAATATTTAGTTTAAAGGAACTAGAACAACATATATAGATTTGTCTTTTAAAATACTATAAAAAAGTAAACATGCATTTATTT

Reverse complement sequence

AAATAAATGCATGTTTACTTTTTTATAGTATTTTAAAAGACAAATCTATATATGTTGTTCTAGTTCCTTTAAACTAAATATTTTTAAAGTTATTGATAGT[C/T]
TAAGTTATAAAAGTTTGACTTCAACCTTATCTAAAACGTTAATTAAACCGGAGGGAGTACTGCTAGAAAAGCATTGGAACCCATACAGTGCAATCCGAAC

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	78.40%	16.60%	3.30%	1.71%	NA
All Indica	2759	90.20%	1.40%	5.47%	2.90%	NA
All Japonica	1512	59.50%	40.30%	0.07%	0.07%	NA
Aus	269	56.10%	43.10%	0.74%	0.00%	NA
Indica I	595	86.40%	0.00%	11.60%	2.02%	NA
Indica II	465	90.10%	0.20%	4.95%	4.73%	NA
Indica III	913	92.70%	1.90%	3.40%	2.08%	NA
Indica Intermediate	786	90.30%	2.70%	3.56%	3.44%	NA
Temperate Japonica	767	87.50%	12.40%	0.00%	0.13%	NA
Tropical Japonica	504	13.70%	86.10%	0.20%	0.00%	NA
Japonica Intermediate	241	66.40%	33.60%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	6.20%	1.04%	0.00%	NA
Intermediate	90	83.30%	15.60%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1002857039	G -> A	LOC_Os10g05690.1	upstream_gene_variant ; 1230.0bp to feature; MODIFIER	silent_mutation	Average:41.016; most accessible tissue: Callus, score: 85.026	N	N	N	N
vg1002857039	G -> A	LOC_Os10g05690-LOC_Os10g05695	intergenic_region ; MODIFIER	silent_mutation	Average:41.016; most accessible tissue: Callus, score: 85.026	N	N	N	N
vg1002857039	G -> DEL	N	N	silent_mutation	Average:41.016; most accessible tissue: Callus, score: 85.026	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002857039	1.86E-06	9.38E-10	mr1220	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
vg1002857039	NA	1.89E-06	mr1220	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
vg1002857039	NA	3.85E-09	mr1248	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
vg1002857039	NA	3.00E-06	mr1736	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