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Detailed information for vg1016561016:

Variant ID: vg1016561016 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 16561016
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 118. )

Flanking Sequence (100 bp) in Reference Genome:

GTGGATTCGAGCGGAATGGCGAACCCTAGTTTGCCGGCGCAGTTCTTTACTGTAGCAGGGAGTGGGGAAAATGGCGAGAGTTCCGGCGGGGAAGACGAAG[C/T]
GTCGCTTCAATCTCGGGATTTCTTGTTAAGGGTATCGGAGGTGCGAATGGGCTTAGGCCTGAACAGTACCTCAGCCCAGTACTTTGACAGCGTGGCCCAT

Reverse complement sequence

ATGGGCCACGCTGTCAAAGTACTGGGCTGAGGTACTGTTCAGGCCTAAGCCCATTCGCACCTCCGATACCCTTAACAAGAAATCCCGAGATTGAAGCGAC[G/A]
CTTCGTCTTCCCCGCCGGAACTCTCGCCATTTTCCCCACTCCCTGCTACAGTAAAGAACTGCGCCGGCAAACTAGGGTTCGCCATTCCGCTCGAATCCAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.10%	1.40%	19.13%	17.46%	NA
All Indica	2759	41.90%	2.20%	27.36%	28.45%	NA
All Japonica	1512	89.90%	0.10%	8.00%	2.05%	NA
Aus	269	93.30%	0.40%	5.95%	0.37%	NA
Indica I	595	51.90%	0.30%	28.24%	19.50%	NA
Indica II	465	23.00%	1.50%	26.02%	49.46%	NA
Indica III	913	40.60%	3.50%	31.98%	23.88%	NA
Indica Intermediate	786	47.10%	2.70%	22.14%	28.12%	NA
Temperate Japonica	767	93.00%	0.00%	5.08%	1.96%	NA
Tropical Japonica	504	84.90%	0.00%	13.69%	1.39%	NA
Japonica Intermediate	241	90.50%	0.40%	5.39%	3.73%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	77.80%	0.00%	13.33%	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
vg1016561016	C -> T	LOC_Os10g31600.1	upstream_gene_variant ; 203.0bp to feature; MODIFIER	silent_mutation	Average:13.088; most accessible tissue: Zhenshan97 young leaf, score: 19.578	N	N	N	N
vg1016561016	C -> T	LOC_Os10g31610.1	upstream_gene_variant ; 1680.0bp to feature; MODIFIER	silent_mutation	Average:13.088; most accessible tissue: Zhenshan97 young leaf, score: 19.578	N	N	N	N
vg1016561016	C -> T	LOC_Os10g31590.1	downstream_gene_variant ; 3441.0bp to feature; MODIFIER	silent_mutation	Average:13.088; most accessible tissue: Zhenshan97 young leaf, score: 19.578	N	N	N	N
vg1016561016	C -> T	LOC_Os10g31600-LOC_Os10g31610	intergenic_region ; MODIFIER	silent_mutation	Average:13.088; most accessible tissue: Zhenshan97 young leaf, score: 19.578	N	N	N	N
vg1016561016	C -> DEL	N	N	silent_mutation	Average:13.088; most accessible tissue: Zhenshan97 young leaf, score: 19.578	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1016561016	3.26E-06	3.25E-06	mr1396	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