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Detailed information for vg0316504140:

Variant ID: vg0316504140 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16504140
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.72, C: 0.28, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

TACAAAACCGTGTAAACGAGGTCCCTCGGCAGCACTGTGCTCGGTTTTGGCTGACGTGGCGCCTACGTTGCTCCTTTGACTATGTTTTCGTCCCACGTGA[C/T]
ATTGACGTGGCGCTTACATGACAATTCGATACCCAAAAATAATAAAAACGTGGGACCCACATGCCAAATACACAAAATAATAAAAAATGATGGGGCCCAT

Reverse complement sequence

ATGGGCCCCATCATTTTTTATTATTTTGTGTATTTGGCATGTGGGTCCCACGTTTTTATTATTTTTGGGTATCGAATTGTCATGTAAGCGCCACGTCAAT[G/A]
TCACGTGGGACGAAAACATAGTCAAAGGAGCAACGTAGGCGCCACGTCAGCCAAAACCGAGCACAGTGCTGCCGAGGGACCTCGTTTACACGGTTTTGTA

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	62.60%	16.50%	1.88%	19.02%	NA
All Indica	2759	79.20%	11.40%	1.12%	8.23%	NA
All Japonica	1512	32.70%	24.50%	3.57%	39.15%	NA
Aus	269	76.60%	1.10%	0.74%	21.56%	NA
Indica I	595	62.00%	35.60%	0.00%	2.35%	NA
Indica II	465	92.50%	4.10%	0.65%	2.80%	NA
Indica III	913	84.30%	2.60%	0.99%	12.05%	NA
Indica Intermediate	786	78.50%	7.60%	2.42%	11.45%	NA
Temperate Japonica	767	6.80%	33.80%	5.35%	54.11%	NA
Tropical Japonica	504	65.90%	13.10%	1.79%	19.25%	NA
Japonica Intermediate	241	46.10%	19.10%	1.66%	33.20%	NA
VI/Aromatic	96	13.50%	80.20%	0.00%	6.25%	NA
Intermediate	90	64.40%	15.60%	2.22%	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
vg0316504140	C -> T	LOC_Os03g29045.1	upstream_gene_variant ; 348.0bp to feature; MODIFIER	silent_mutation	Average:68.977; most accessible tissue: Zhenshan97 young leaf, score: 80.056	N	N	N	N
vg0316504140	C -> T	LOC_Os03g29035-LOC_Os03g29045	intergenic_region ; MODIFIER	silent_mutation	Average:68.977; most accessible tissue: Zhenshan97 young leaf, score: 80.056	N	N	N	N
vg0316504140	C -> DEL	N	N	silent_mutation	Average:68.977; most accessible tissue: Zhenshan97 young leaf, score: 80.056	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316504140	NA	2.22E-06	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
vg0316504140	NA	7.62E-06	mr1220_2	Jap_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
vg0316504140	NA	1.96E-07	mr1456_2	Jap_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
vg0316504140	NA	1.13E-07	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
vg0316504140	6.59E-06	6.59E-06	mr1547_2	Jap_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
vg0316504140	NA	3.07E-09	mr1624_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
vg0316504140	3.23E-06	3.23E-06	mr1681_2	Jap_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
vg0316504140	4.99E-06	4.98E-06	mr1719_2	Jap_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
vg0316504140	NA	6.94E-06	mr1739_2	Jap_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
vg0316504140	NA	8.14E-07	mr1740_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
vg0316504140	NA	1.19E-06	mr1780_2	Jap_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
vg0316504140	NA	5.29E-06	mr1785_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
vg0316504140	1.83E-06	1.83E-06	mr1895_2	Jap_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
vg0316504140	7.14E-06	7.14E-06	mr1914_2	Jap_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