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Detailed information for vg0200409865:

Variant ID: vg0200409865 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 409865
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.50, T: 0.49, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

ACGCCGTTGACTTTTTTTCAACGTTTGATCATTCGTCTTATTCAAAAAGTTTATATAATTATAATTTATTTTATTATGACTTGATTTATCATCAAATATT[T/C]
TTTAAGCATGACATAAATATGTTCATATTTACACAAAAAATTTGAATAAAACGAATAGTCAAACGTTGGTCGAAAAGTCAATGGCGTCATACATTAAAAT

Reverse complement sequence

ATTTTAATGTATGACGCCATTGACTTTTCGACCAACGTTTGACTATTCGTTTTATTCAAATTTTTTGTGTAAATATGAACATATTTATGTCATGCTTAAA[A/G]
AATATTTGATGATAAATCAAGTCATAATAAAATAAATTATAATTATATAAACTTTTTGAATAAGACGAATGATCAAACGTTGAAAAAAAGTCAACGGCGT

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	77.10%	7.70%	4.36%	10.83%	NA
All Indica	2759	69.10%	11.00%	6.67%	13.23%	NA
All Japonica	1512	99.30%	0.10%	0.07%	0.46%	NA
Aus	269	39.40%	11.20%	7.43%	42.01%	NA
Indica I	595	56.30%	12.40%	7.56%	23.70%	NA
Indica II	465	82.40%	5.20%	6.24%	6.24%	NA
Indica III	913	72.70%	12.90%	4.05%	10.30%	NA
Indica Intermediate	786	66.80%	11.10%	9.29%	12.85%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.00%	0.00%	0.00%	0.99%	NA
Japonica Intermediate	241	98.80%	0.40%	0.00%	0.83%	NA
VI/Aromatic	96	55.20%	24.00%	1.04%	19.79%	NA
Intermediate	90	82.20%	8.90%	0.00%	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
vg0200409865	T -> DEL	N	N	silent_mutation	Average:71.887; most accessible tissue: Minghui63 flag leaf, score: 85.151	N	N	N	N
vg0200409865	T -> C	LOC_Os02g01730.1	upstream_gene_variant ; 3174.0bp to feature; MODIFIER	silent_mutation	Average:71.887; most accessible tissue: Minghui63 flag leaf, score: 85.151	N	N	N	N
vg0200409865	T -> C	LOC_Os02g01740.1	upstream_gene_variant ; 796.0bp to feature; MODIFIER	silent_mutation	Average:71.887; most accessible tissue: Minghui63 flag leaf, score: 85.151	N	N	N	N
vg0200409865	T -> C	LOC_Os02g01730-LOC_Os02g01740	intergenic_region ; MODIFIER	silent_mutation	Average:71.887; most accessible tissue: Minghui63 flag leaf, score: 85.151	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0200409865	NA	9.21E-06	mr1308	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