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Detailed information for vg0406404953:

Variant ID: vg0406404953 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6404953
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.07, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAGGAGAGGAAAGCACATGAAAGCATGGAGAATTTATTTTGGTGGTAATATGGAAATGGAATGGAATATTGCTTAGCTCCCAGTGTAGGAGTTTAGCA[T/C]
GTGCATAAATGTGGGTGTATGATCTTGATCATAGAGCATGAGAAGTATCTACACAAGTCACAAGAGTTTGACAAAGTTCAATGGAATGGCAAGCAACCAA

Reverse complement sequence

TTGGTTGCTTGCCATTCCATTGAACTTTGTCAAACTCTTGTGACTTGTGTAGATACTTCTCATGCTCTATGATCAAGATCATACACCCACATTTATGCAC[A/G]
TGCTAAACTCCTACACTGGGAGCTAAGCAATATTCCATTCCATTTCCATATTACCACCAAAATAAATTCTCCATGCTTTCATGTGCTTTCCTCTCCTAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.70%	10.00%	1.57%	0.72%	NA
All Indica	2759	86.60%	10.90%	1.23%	1.23%	NA
All Japonica	1512	97.00%	2.60%	0.40%	0.00%	NA
Aus	269	65.10%	32.70%	2.23%	0.00%	NA
Indica I	595	91.90%	7.70%	0.34%	0.00%	NA
Indica II	465	86.20%	2.80%	4.52%	6.45%	NA
Indica III	913	84.00%	15.60%	0.22%	0.22%	NA
Indica Intermediate	786	85.80%	12.80%	1.15%	0.25%	NA
Temperate Japonica	767	95.80%	3.70%	0.52%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	95.40%	3.70%	0.83%	0.00%	NA
VI/Aromatic	96	38.50%	36.50%	25.00%	0.00%	NA
Intermediate	90	84.40%	11.10%	4.44%	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
vg0406404953	T -> C	LOC_Os04g11680.1	upstream_gene_variant ; 3848.0bp to feature; MODIFIER	silent_mutation	Average:25.512; most accessible tissue: Minghui63 young leaf, score: 39.381	N	N	N	N
vg0406404953	T -> C	LOC_Os04g11670.1	downstream_gene_variant ; 2744.0bp to feature; MODIFIER	silent_mutation	Average:25.512; most accessible tissue: Minghui63 young leaf, score: 39.381	N	N	N	N
vg0406404953	T -> C	LOC_Os04g11670-LOC_Os04g11680	intergenic_region ; MODIFIER	silent_mutation	Average:25.512; most accessible tissue: Minghui63 young leaf, score: 39.381	N	N	N	N
vg0406404953	T -> DEL	N	N	silent_mutation	Average:25.512; most accessible tissue: Minghui63 young leaf, score: 39.381	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406404953	6.79E-07	NA	mr1913	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
vg0406404953	NA	7.03E-07	mr1126_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