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Detailed information for vg0316224648:

Variant ID: vg0316224648 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16224648
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

CATTTCCAACCCAAAGGAAATGCACAATATTACTCTGAACACCAACAGGCATCGTCATCTTCTTCCTCCTCCCTCCTTCGGTCAGCTCCGGGAGGATGAG[C/T]
AGCTTGCAGAGGGCATCAATGGAGGATGAGCAGCTTGCAGAGCTCGTACAGGGTCGTGGGAGCATCTGGCGCTCCCGTGCGCCACGTCGTCGTCGCCGCC

Reverse complement sequence

GGCGGCGACGACGACGTGGCGCACGGGAGCGCCAGATGCTCCCACGACCCTGTACGAGCTCTGCAAGCTGCTCATCCTCCATTGATGCCCTCTGCAAGCT[G/A]
CTCATCCTCCCGGAGCTGACCGAAGGAGGGAGGAGGAAGAAGATGACGATGCCTGTTGGTGTTCAGAGTAATATTGTGCATTTCCTTTGGGTTGGAAATG

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	55.60%	0.40%	5.10%	38.87%	NA
All Indica	2759	32.00%	0.60%	7.97%	59.44%	NA
All Japonica	1512	89.40%	0.00%	0.66%	9.92%	NA
Aus	269	94.80%	0.00%	2.23%	2.97%	NA
Indica I	595	47.10%	0.30%	3.19%	49.41%	NA
Indica II	465	14.40%	0.40%	10.11%	75.05%	NA
Indica III	913	29.70%	0.90%	11.28%	58.16%	NA
Indica Intermediate	786	33.70%	0.50%	6.49%	59.29%	NA
Temperate Japonica	767	96.90%	0.00%	0.00%	3.13%	NA
Tropical Japonica	504	81.70%	0.00%	1.39%	16.87%	NA
Japonica Intermediate	241	81.70%	0.00%	1.24%	17.01%	NA
VI/Aromatic	96	88.50%	1.00%	2.08%	8.33%	NA
Intermediate	90	61.10%	1.10%	3.33%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0316224648	C -> T	LOC_Os03g28180.1	upstream_gene_variant ; 2711.0bp to feature; MODIFIER	silent_mutation	Average:50.4; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N
vg0316224648	C -> T	LOC_Os03g28204.1	upstream_gene_variant ; 4765.0bp to feature; MODIFIER	silent_mutation	Average:50.4; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N
vg0316224648	C -> T	LOC_Os03g28190.1	downstream_gene_variant ; 3009.0bp to feature; MODIFIER	silent_mutation	Average:50.4; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N
vg0316224648	C -> T	LOC_Os03g28180-LOC_Os03g28190	intergenic_region ; MODIFIER	silent_mutation	Average:50.4; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N
vg0316224648	C -> DEL	N	N	silent_mutation	Average:50.4; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316224648	NA	9.95E-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
vg0316224648	NA	5.04E-08	mr1285	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
vg0316224648	NA	1.46E-06	mr1358	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
vg0316224648	NA	3.91E-06	mr1432	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
vg0316224648	NA	5.10E-06	mr1534	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
vg0316224648	NA	8.48E-06	mr1956	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