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Detailed information for vg0418589258:

Variant ID: vg0418589258 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 18589258
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.14, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

AGCAGCTATATAATCTTCAGGTTCCAGGCGGCAGAGTGCCAACAAATTGATGAGGGTATATGCATCATAGCAGGCATCATATTATGTTCTCTTTTTTTAC[T/C]
ACAGTTTTCACCTTGGGAGAAGCTGAAACTGCATTGCTGCTATAGAAGCAAAGGACATGAAACTAATTATCAACATAGATAACAGCATATATAGTTTCAT

Reverse complement sequence

ATGAAACTATATATGCTGTTATCTATGTTGATAATTAGTTTCATGTCCTTTGCTTCTATAGCAGCAATGCAGTTTCAGCTTCTCCCAAGGTGAAAACTGT[A/G]
GTAAAAAAAGAGAACATAATATGATGCCTGCTATGATGCATATACCCTCATCAATTTGTTGGCACTCTGCCGCCTGGAACCTGAAGATTATATAGCTGCT

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	30.30%	22.10%	0.61%	47.00%	NA
All Indica	2759	9.80%	13.60%	0.69%	75.90%	NA
All Japonica	1512	71.00%	28.40%	0.46%	0.13%	NA
Aus	269	0.00%	61.00%	0.00%	39.03%	NA
Indica I	595	24.90%	14.80%	0.67%	59.66%	NA
Indica II	465	12.50%	30.50%	1.08%	55.91%	NA
Indica III	913	1.80%	1.90%	0.00%	96.39%	NA
Indica Intermediate	786	6.20%	16.30%	1.27%	76.21%	NA
Temperate Japonica	767	56.20%	42.90%	0.78%	0.13%	NA
Tropical Japonica	504	86.90%	12.70%	0.20%	0.20%	NA
Japonica Intermediate	241	84.60%	15.40%	0.00%	0.00%	NA
VI/Aromatic	96	56.20%	39.60%	0.00%	4.17%	NA
Intermediate	90	38.90%	40.00%	3.33%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0418589258	T -> C	LOC_Os04g31090.1	downstream_gene_variant ; 415.0bp to feature; MODIFIER	silent_mutation	Average:38.65; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0418589258	T -> C	LOC_Os04g31080-LOC_Os04g31090	intergenic_region ; MODIFIER	silent_mutation	Average:38.65; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0418589258	T -> DEL	N	N	silent_mutation	Average:38.65; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0418589258	NA	2.95E-08	mr1403	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
vg0418589258	2.62E-07	4.92E-10	mr1851	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
vg0418589258	1.52E-06	2.07E-09	mr1864	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
vg0418589258	1.24E-06	2.69E-06	mr1851_2	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