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Detailed information for vg0217388064:

Variant ID: vg0217388064 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17388064
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.14, C: 0.11, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

AAACCAAATACATCAAAGATCTACTCAAGAGGTTTGGCTTGGAGGATGCGAAGCCCATCAAGACACCTATGGCAACCAACGGGCATCTCGACCTTGATGA[C/T]
GGAGGTAAACCGGTAGATTTAAAGCTTTATCGTTCTATGATTGGTAGCTTGCTTTACCTTACAGCATCTAGGCCGGATATCATGATTAGTGTTTGCATGT

Reverse complement sequence

ACATGCAAACACTAATCATGATATCCGGCCTAGATGCTGTAAGGTAAAGCAAGCTACCAATCATAGAACGATAAAGCTTTAAATCTACCGGTTTACCTCC[G/A]
TCATCAAGGTCGAGATGCCCGTTGGTTGCCATAGGTGTCTTGATGGGCTTCGCATCCTCCAAGCCAAACCTCTTGAGTAGATCTTTGATGTATTTGGTTT

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	35.00%	1.40%	21.98%	41.58%	NA
All Indica	2759	4.90%	2.40%	31.13%	61.62%	NA
All Japonica	1512	97.40%	0.00%	0.40%	2.25%	NA
Aus	269	0.70%	0.00%	59.11%	40.15%	NA
Indica I	595	2.40%	0.20%	20.00%	77.48%	NA
Indica II	465	5.40%	6.90%	20.43%	67.31%	NA
Indica III	913	7.30%	2.00%	46.99%	43.70%	NA
Indica Intermediate	786	3.70%	1.80%	27.48%	67.05%	NA
Temperate Japonica	767	98.70%	0.00%	0.13%	1.17%	NA
Tropical Japonica	504	95.80%	0.00%	0.40%	3.77%	NA
Japonica Intermediate	241	96.30%	0.00%	1.24%	2.49%	NA
VI/Aromatic	96	10.40%	0.00%	1.04%	88.54%	NA
Intermediate	90	40.00%	2.20%	15.56%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0217388064	C -> T	LOC_Os02g29260.1	synonymous_variant ; p.Asp1143Asp; LOW	synonymous_codon	Average:24.795; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N
vg0217388064	C -> DEL	LOC_Os02g29260.1	N	frameshift_variant	Average:24.795; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217388064	1.19E-06	1.19E-06	mr1412	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