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Detailed information for vg0202540568:

Variant ID: vg0202540568 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2540568
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.25, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TCTGCTATATATCTTGCCTTCTAGAAAGTATTTTTCAGGAACAATTGAGCACTTGAGTAGGATGTGGTCGAGTACACTGCATTATCAAGAACGTTCTTGA[C/T]
AAATGCAGAGTCGTCGCGCCCAACCAACCAACGAAGACCGACGACCTATCTCATACACCGGCCATGGCTGGACTACTCGAGAAAAGGTTGTTAACGGATA

Reverse complement sequence

TATCCGTTAACAACCTTTTCTCGAGTAGTCCAGCCATGGCCGGTGTATGAGATAGGTCGTCGGTCTTCGTTGGTTGGTTGGGCGCGACGACTCTGCATTT[G/A]
TCAAGAACGTTCTTGATAATGCAGTGTACTCGACCACATCCTACTCAAGTGCTCAATTGTTCCTGAAAAATACTTTCTAGAAGGCAAGATATATAGCAGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.60%	23.40%	0.02%	0.00%	NA
All Indica	2759	96.20%	3.80%	0.00%	0.00%	NA
All Japonica	1512	42.90%	57.10%	0.00%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	97.40%	2.60%	0.00%	0.00%	NA
Indica III	913	95.50%	4.50%	0.00%	0.00%	NA
Indica Intermediate	786	93.80%	6.20%	0.00%	0.00%	NA
Temperate Japonica	767	8.60%	91.40%	0.00%	0.00%	NA
Tropical Japonica	504	89.90%	10.10%	0.00%	0.00%	NA
Japonica Intermediate	241	53.90%	46.10%	0.00%	0.00%	NA
VI/Aromatic	96	5.20%	93.80%	1.04%	0.00%	NA
Intermediate	90	63.30%	36.70%	0.00%	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
vg0202540568	C -> T	LOC_Os02g05270.1	upstream_gene_variant ; 4393.0bp to feature; MODIFIER	silent_mutation	Average:58.062; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0202540568	C -> T	LOC_Os02g05280.1	downstream_gene_variant ; 1898.0bp to feature; MODIFIER	silent_mutation	Average:58.062; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0202540568	C -> T	LOC_Os02g05300.1	downstream_gene_variant ; 1522.0bp to feature; MODIFIER	silent_mutation	Average:58.062; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0202540568	C -> T	LOC_Os02g05290.1	intron_variant ; MODIFIER	silent_mutation	Average:58.062; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202540568	NA	3.87E-06	mr1977	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