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Detailed information for vg0417243569:

Variant ID: vg0417243569 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17243569
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.59, C: 0.41, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

CCTAGTTAAGCCTCTGCTCAACTGAACCCATAAACGATAGTTTACACTGCTTTTTGCTATTTTTCATTTTGCGAAGTAGGGGATACATTGAAGAATGCAT[C/T]
CATGTCCCAATCGACATTTCCATTCGAGCTTGCACGCTGTTTTGGATGCATCAAGTGCTCTCATCAAACACTAGGACATAACATTTGAAGATGTGATGGA

Reverse complement sequence

TCCATCACATCTTCAAATGTTATGTCCTAGTGTTTGATGAGAGCACTTGATGCATCCAAAACAGCGTGCAAGCTCGAATGGAAATGTCGATTGGGACATG[G/A]
ATGCATTCTTCAATGTATCCCCTACTTCGCAAAATGAAAAATAGCAAAAAGCAGTGTAAACTATCGTTTATGGGTTCAGTTGAGCAGAGGCTTAACTAGG

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	84.30%	11.90%	0.51%	3.24%	NA
All Indica	2759	93.70%	5.00%	0.18%	1.16%	NA
All Japonica	1512	74.50%	25.40%	0.00%	0.07%	NA
Aus	269	50.60%	9.70%	6.32%	33.46%	NA
Indica I	595	79.00%	21.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.20%	0.22%	0.22%	NA
Indica III	913	97.90%	0.00%	0.11%	1.97%	NA
Indica Intermediate	786	96.60%	1.40%	0.38%	1.65%	NA
Temperate Japonica	767	57.20%	42.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	0.80%	0.00%	0.20%	NA
Japonica Intermediate	241	78.40%	21.60%	0.00%	0.00%	NA
VI/Aromatic	96	64.60%	2.10%	2.08%	31.25%	NA
Intermediate	90	84.40%	15.60%	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
vg0417243569	C -> DEL	N	N	silent_mutation	Average:32.576; most accessible tissue: Zhenshan97 young leaf, score: 61.964	N	N	N	N
vg0417243569	C -> T	LOC_Os04g29080-LOC_Os04g29090	intergenic_region ; MODIFIER	silent_mutation	Average:32.576; most accessible tissue: Zhenshan97 young leaf, score: 61.964	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417243569	1.53E-06	1.52E-06	mr1703	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