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Detailed information for vg0114587514:

Variant ID: vg0114587514 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14587514
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TACATTAATTTAAGTGTTGCATTCATGGTAAGAACAAGAACAACTATACAGAGTTTTTGTATGTACGAAGTTGAGTACTCACATATGTCAACGTCATTTA[C/T]
CTAGACAAATTTGAAGAATTCAGCAGAAGAAAGATTATGTTCTTGGTTTTCCATAGTCCACATCATGGTCCACATTTGGAGGGAAAATGAAAATTGAGAC

Reverse complement sequence

GTCTCAATTTTCATTTTCCCTCCAAATGTGGACCATGATGTGGACTATGGAAAACCAAGAACATAATCTTTCTTCTGCTGAATTCTTCAAATTTGTCTAG[G/A]
TAAATGACGTTGACATATGTGAGTACTCAACTTCGTACATACAAAAACTCTGTATAGTTGTTCTTGTTCTTACCATGAATGCAACACTTAAATTAATGTA

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	60.70%	17.90%	0.72%	20.72%	NA
All Indica	2759	34.00%	30.00%	1.20%	34.87%	NA
All Japonica	1512	99.80%	0.00%	0.00%	0.20%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	42.40%	6.70%	2.02%	48.91%	NA
Indica II	465	22.60%	46.20%	0.65%	30.54%	NA
Indica III	913	33.50%	36.40%	0.55%	29.57%	NA
Indica Intermediate	786	34.90%	30.50%	1.65%	32.95%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	66.70%	16.70%	1.11%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114587514	C -> T	LOC_Os01g25740.1	splice_donor_variant&intron_variant ; HIGH	silent_mutation	Average:63.741; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg0114587514	C -> DEL	N	N	silent_mutation	Average:63.741; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114587514	NA	2.40E-06	mr1428_2	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
vg0114587514	NA	3.49E-06	mr1654_2	Ind_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