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Detailed information for vg0406529240:

Variant ID: vg0406529240 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6529240
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTAGATAATTTATAGTTAAAGTTGTAATATATTATATGTACTCATCCAAATTTGCAATAGTAGTATTGTTTTAGAGGTCATATCTAAATAGGTACAAA[C/T]
AGTCCGTAGCAAAGAACATGATGCGGCTCAATGAGTGTCATTGTCCTAGATAAAGAATAGAAAGAGCTAGCCAAAATGATTTTTAACTTAGCTTCCGTCA

Reverse complement sequence

TGACGGAAGCTAAGTTAAAAATCATTTTGGCTAGCTCTTTCTATTCTTTATCTAGGACAATGACACTCATTGAGCCGCATCATGTTCTTTGCTACGGACT[G/A]
TTTGTACCTATTTAGATATGACCTCTAAAACAATACTACTATTGCAAATTTGGATGAGTACATATAATATATTACAACTTTAACTATAAATTATCTAACG

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	89.20%	10.80%	0.04%	0.00%	NA
All Indica	2759	85.80%	14.20%	0.04%	0.00%	NA
All Japonica	1512	99.50%	0.40%	0.07%	0.00%	NA
Aus	269	72.50%	27.50%	0.00%	0.00%	NA
Indica I	595	82.00%	18.00%	0.00%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	83.10%	16.90%	0.00%	0.00%	NA
Indica Intermediate	786	84.20%	15.60%	0.13%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	69.80%	30.20%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0406529240	C -> T	LOC_Os04g11900.1	upstream_gene_variant ; 2882.0bp to feature; MODIFIER	silent_mutation	Average:15.927; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0406529240	C -> T	LOC_Os04g11910.1	intron_variant ; MODIFIER	silent_mutation	Average:15.927; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406529240	1.56E-08	7.54E-09	mr1946	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