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Detailed information for vg0314646020:

Variant ID: vg0314646020 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14646020
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

TTATCATGGCGCCGTGAAGAGACATGACGCCGAGAGCGATTCACGTTGTCTCGTGTGCGTTGTGCTTCCCGGCGGCCGTTGATTTGATCTCGAAGATCGC[C/T]
AGTGCCGCGAGGTGGAGGGGTAGCTTGTTGAGGTGATTCCCTCCGTTCCGGATCTTCACCATTGGCCTCTCCAGTTGGTGGCTGCTCCTAGTGTGCTGCG

Reverse complement sequence

CGCAGCACACTAGGAGCAGCCACCAACTGGAGAGGCCAATGGTGAAGATCCGGAACGGAGGGAATCACCTCAACAAGCTACCCCTCCACCTCGCGGCACT[G/A]
GCGATCTTCGAGATCAAATCAACGGCCGCCGGGAAGCACAACGCACACGAGACAACGTGAATCGCTCTCGGCGTCATGTCTCTTCACGGCGCCATGATAA

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	79.50%	1.90%	18.60%	0.00%	NA
All Indica	2759	69.40%	2.80%	27.76%	0.00%	NA
All Japonica	1512	99.20%	0.00%	0.79%	0.00%	NA
Aus	269	65.80%	3.70%	30.48%	0.00%	NA
Indica I	595	66.20%	1.20%	32.61%	0.00%	NA
Indica II	465	35.30%	5.40%	59.35%	0.00%	NA
Indica III	913	91.50%	1.50%	7.01%	0.00%	NA
Indica Intermediate	786	66.50%	3.90%	29.52%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	98.20%	0.00%	1.79%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	95.80%	0.00%	4.17%	0.00%	NA
Intermediate	90	81.10%	2.20%	16.67%	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
vg0314646020	C -> T	LOC_Os03g25590.1	intron_variant ; MODIFIER	silent_mutation	Average:39.565; most accessible tissue: Minghui63 young leaf, score: 67.374	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314646020	NA	1.09E-08	mr1542	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
vg0314646020	1.79E-06	NA	mr1542_2	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
vg0314646020	NA	2.43E-10	mr1542_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