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Detailed information for vg0316618971:

Variant ID: vg0316618971 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16618971
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAAAGGAGGCTGAAGATCGACGGCAGCGCGCCTTGGAATCCGGGCGACAAGCGAGAGACCTCATCGGGCAACAAGACGTCGATGGAACAGCGGTTTTTC[G/T]
CACCCCCTAGCAGAACGCGGTTGCAGCAATCACTCTCCTCGACACCCTCCTCAAGGAAGACACACTCAACCAAGCTGATCATGTTGTCAACATCTTGAAC

Reverse complement sequence

GTTCAAGATGTTGACAACATGATCAGCTTGGTTGAGTGTGTCTTCCTTGAGGAGGGTGTCGAGGAGAGTGATTGCTGCAACCGCGTTCTGCTAGGGGGTG[C/A]
GAAAAACCGCTGTTCCATCGACGTCTTGTTGCCCGATGAGGTCTCTCGCTTGTCGCCCGGATTCCAAGGCGCGCTGCCGTCGATCTTCAGCCTCCTTTGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.60%	4.80%	0.51%	0.00%	NA
All Indica	2759	91.60%	7.60%	0.83%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	94.50%	4.90%	0.67%	0.00%	NA
Indica II	465	98.10%	1.70%	0.22%	0.00%	NA
Indica III	913	86.70%	11.60%	1.64%	0.00%	NA
Indica Intermediate	786	91.10%	8.50%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	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
vg0316618971	G -> T	LOC_Os03g29220.1	upstream_gene_variant ; 1967.0bp to feature; MODIFIER	silent_mutation	Average:57.185; most accessible tissue: Zhenshan97 flag leaf, score: 76.356	N	N	N	N
vg0316618971	G -> T	LOC_Os03g29224.1	upstream_gene_variant ; 2607.0bp to feature; MODIFIER	silent_mutation	Average:57.185; most accessible tissue: Zhenshan97 flag leaf, score: 76.356	N	N	N	N
vg0316618971	G -> T	LOC_Os03g29222.1	intron_variant ; MODIFIER	silent_mutation	Average:57.185; most accessible tissue: Zhenshan97 flag leaf, score: 76.356	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316618971	NA	3.88E-06	mr1515	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
vg0316618971	6.38E-07	2.04E-07	mr1917	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