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Detailed information for vg0210784018:

Variant ID: vg0210784018 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10784018
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.21, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

GATAACAAGCTAGTCACATCCAGGATCATCATGGGAGGGCTGGGAATTCTCGAAATGGAAAAATTCACATCTACGCTTAGGCTACGATGGTTGTGGCTGT[T/C]
TGATACAAGCAGACCTTGGGAGCTGATGGAGATGCCTTGCAATATGCGAGATGTACAACTCTTCCAGGCATGCACAAAAATCACAGTAGGAGATGGCAAA

Reverse complement sequence

TTTGCCATCTCCTACTGTGATTTTTGTGCATGCCTGGAAGAGTTGTACATCTCGCATATTGCAAGGCATCTCCATCAGCTCCCAAGGTCTGCTTGTATCA[A/G]
ACAGCCACAACCATCGTAGCCTAAGCGTAGATGTGAATTTTTCCATTTCGAGAATTCCCAGCCCTCCCATGATGATCCTGGATGTGACTAGCTTGTTATC

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	74.10%	21.20%	4.66%	0.00%	NA
All Indica	2759	75.60%	22.50%	1.85%	0.00%	NA
All Japonica	1512	73.50%	16.30%	10.12%	0.00%	NA
Aus	269	51.70%	45.40%	2.97%	0.00%	NA
Indica I	595	77.50%	17.50%	5.04%	0.00%	NA
Indica II	465	68.40%	30.10%	1.51%	0.00%	NA
Indica III	913	77.30%	22.50%	0.22%	0.00%	NA
Indica Intermediate	786	76.60%	21.90%	1.53%	0.00%	NA
Temperate Japonica	767	56.20%	28.30%	15.51%	0.00%	NA
Tropical Japonica	504	93.50%	3.40%	3.17%	0.00%	NA
Japonica Intermediate	241	87.10%	5.40%	7.47%	0.00%	NA
VI/Aromatic	96	95.80%	0.00%	4.17%	0.00%	NA
Intermediate	90	82.20%	13.30%	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
vg0210784018	T -> C	LOC_Os02g18510.1	upstream_gene_variant ; 3260.0bp to feature; MODIFIER	silent_mutation	Average:62.803; most accessible tissue: Zhenshan97 root, score: 89.905	N	N	N	N
vg0210784018	T -> C	LOC_Os02g18515.1	upstream_gene_variant ; 3270.0bp to feature; MODIFIER	silent_mutation	Average:62.803; most accessible tissue: Zhenshan97 root, score: 89.905	N	N	N	N
vg0210784018	T -> C	LOC_Os02g18510-LOC_Os02g18515	intergenic_region ; MODIFIER	silent_mutation	Average:62.803; most accessible tissue: Zhenshan97 root, score: 89.905	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210784018	4.82E-06	4.82E-06	mr1587	Jap_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