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Detailed information for vg1011061499:

Variant ID: vg1011061499 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11061499
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.62, A: 0.37, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTTTTAAATCTGAGTTGAAAGTTTTCAAATATGAGTTGAAAGTTTTCAAGTCGGTGTTGAAAGTATTCAAATCTGGGTTGAATGTTTACACATATAT[A/G]
GAAAAATTCGGAAAAAAGAAAAACTAACCGTGTCTTGCCGCCTATTGGGCCGTGTGGGCTGGCGCGTGCGCGCCGCCGGCGCGTACGCGCCAATTAGGAT

Reverse complement sequence

ATCCTAATTGGCGCGTACGCGCCGGCGGCGCGCACGCGCCAGCCCACACGGCCCAATAGGCGGCAAGACACGGTTAGTTTTTCTTTTTTCCGAATTTTTC[T/C]
ATATATGTGTAAACATTCAACCCAGATTTGAATACTTTCAACACCGACTTGAAAACTTTCAACTCATATTTGAAAACTTTCAACTCAGATTTAAAAATTT

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	89.00%	7.60%	3.09%	0.34%	NA
All Indica	2759	93.10%	3.30%	3.19%	0.40%	NA
All Japonica	1512	99.30%	0.50%	0.20%	0.00%	NA
Aus	269	13.40%	79.90%	6.32%	0.37%	NA
Indica I	595	97.30%	1.50%	1.01%	0.17%	NA
Indica II	465	98.10%	0.60%	0.65%	0.65%	NA
Indica III	913	91.50%	3.10%	4.71%	0.77%	NA
Indica Intermediate	786	88.80%	6.60%	4.58%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	96.70%	2.50%	0.83%	0.00%	NA
VI/Aromatic	96	24.00%	36.50%	35.42%	4.17%	NA
Intermediate	90	84.40%	11.10%	4.44%	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
vg1011061499	A -> G	LOC_Os10g21590.1	upstream_gene_variant ; 3754.0bp to feature; MODIFIER	silent_mutation	Average:27.756; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg1011061499	A -> G	LOC_Os10g21600.1	downstream_gene_variant ; 1581.0bp to feature; MODIFIER	silent_mutation	Average:27.756; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg1011061499	A -> G	LOC_Os10g21600-LOC_Os10g21620	intergenic_region ; MODIFIER	silent_mutation	Average:27.756; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg1011061499	A -> DEL	N	N	silent_mutation	Average:27.756; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011061499	NA	1.33E-06	mr1118	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
vg1011061499	4.46E-06	7.71E-16	mr1552_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