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Detailed information for vg0323588254:

Variant ID: vg0323588254 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 23588254
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TGGAGTGTTCTGTTCAGAGTTGTCACAGTTTTCTTTAGAGCCGTGACACTCTTCGTCGTTTCTTCGAACAACACATAACGACTTGGCTCTACCCTTGCCC[C/T]
GTCTATTAGTGAAACCGAGACCATTTGTATTTGTTATAGCAGCAAGAGGGTCTGAGAAAGGAACACATGGTCGAAATTAGTACGCAAAGAATTTGTGCAT

Reverse complement sequence

ATGCACAAATTCTTTGCGTACTAATTTCGACCATGTGTTCCTTTCTCAGACCCTCTTGCTGCTATAACAAATACAAATGGTCTCGGTTTCACTAATAGAC[G/A]
GGGCAAGGGTAGAGCCAAGTCGTTATGTGTTGTTCGAAGAAACGACGAAGAGTGTCACGGCTCTAAAGAAAACTGTGACAACTCTGAACAGAACACTCCA

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	51.10%	48.40%	0.49%	0.00%	NA
All Indica	2759	79.40%	20.40%	0.18%	0.00%	NA
All Japonica	1512	9.30%	89.80%	0.93%	0.00%	NA
Aus	269	16.00%	84.00%	0.00%	0.00%	NA
Indica I	595	68.90%	30.90%	0.17%	0.00%	NA
Indica II	465	80.20%	19.80%	0.00%	0.00%	NA
Indica III	913	89.20%	10.60%	0.22%	0.00%	NA
Indica Intermediate	786	75.70%	24.00%	0.25%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	25.20%	72.80%	1.98%	0.00%	NA
Japonica Intermediate	241	4.10%	94.20%	1.66%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	42.20%	53.30%	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
vg0323588254	C -> T	LOC_Os03g42380.1	upstream_gene_variant ; 209.0bp to feature; MODIFIER	silent_mutation	Average:35.186; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0323588254	C -> T	LOC_Os03g42400.1	upstream_gene_variant ; 3880.0bp to feature; MODIFIER	silent_mutation	Average:35.186; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0323588254	C -> T	LOC_Os03g42380-LOC_Os03g42400	intergenic_region ; MODIFIER	silent_mutation	Average:35.186; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0323588254	NA	1.29E-08	mr1045	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
vg0323588254	2.63E-06	NA	mr1092	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
vg0323588254	NA	2.31E-12	mr1329	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
vg0323588254	NA	1.43E-06	mr1568	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
vg0323588254	NA	1.33E-09	mr1663	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
vg0323588254	NA	1.36E-07	mr1748	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
vg0323588254	NA	4.24E-07	mr1785	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
vg0323588254	NA	8.60E-06	mr1553_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