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Detailed information for vg1017171887:

Variant ID: vg1017171887 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 17171887
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:

CAAAAGTGCCCGTGCGTTGCACCGGGTGATTACGGAGTGTGTATATTGACCAAAATTGTTGTTTGGTTTAGCAAAAGTGCCCGTGCGTTGCACTGGGAAG[C/T,A]
GCACAGATCAGTAAAAATATGCAAATTAATTAAAACACAAATTCACTGAAATATTTGGTATTTTTAAGTAGGTATGTGTATAATTAAATAAATTTACAAG

Reverse complement sequence

CTTGTAAATTTATTTAATTATACACATACCTACTTAAAAATACCAAATATTTCAGTGAATTTGTGTTTTAATTAATTTGCATATTTTTACTGATCTGTGC[G/A,T]
CTTCCCAGTGCAACGCACGGGCACTTTTGCTAAACCAAACAACAATTTTGGTCAATATACACACTCCGTAATCACCCGGTGCAACGCACGGGCACTTTTG

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	48.70%	24.60%	12.42%	14.24%	A: 0.06%
All Indica	2759	18.30%	39.60%	20.01%	22.00%	A: 0.04%
All Japonica	1512	93.30%	2.20%	1.39%	3.04%	NA
Aus	269	90.00%	5.90%	2.60%	1.49%	NA
Indica I	595	21.70%	21.70%	28.40%	28.24%	NA
Indica II	465	14.80%	28.80%	22.37%	33.98%	NA
Indica III	913	16.90%	56.50%	15.12%	11.50%	NA
Indica Intermediate	786	19.60%	39.90%	17.94%	22.39%	A: 0.13%
Temperate Japonica	767	98.00%	0.40%	0.26%	1.30%	NA
Tropical Japonica	504	95.60%	1.80%	0.79%	1.79%	NA
Japonica Intermediate	241	73.40%	9.10%	6.22%	11.20%	NA
VI/Aromatic	96	95.80%	1.00%	0.00%	3.12%	NA
Intermediate	90	56.70%	18.90%	7.78%	14.44%	A: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1017171887	C -> T	LOC_Os10g32790.1	upstream_gene_variant ; 623.0bp to feature; MODIFIER	silent_mutation	Average:57.128; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg1017171887	C -> T	LOC_Os10g32800.1	upstream_gene_variant ; 3829.0bp to feature; MODIFIER	silent_mutation	Average:57.128; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg1017171887	C -> T	LOC_Os10g32780.1	downstream_gene_variant ; 4737.0bp to feature; MODIFIER	silent_mutation	Average:57.128; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg1017171887	C -> T	LOC_Os10g32790-LOC_Os10g32800	intergenic_region ; MODIFIER	silent_mutation	Average:57.128; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg1017171887	C -> A	LOC_Os10g32790.1	upstream_gene_variant ; 623.0bp to feature; MODIFIER	silent_mutation	Average:57.128; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg1017171887	C -> A	LOC_Os10g32800.1	upstream_gene_variant ; 3829.0bp to feature; MODIFIER	silent_mutation	Average:57.128; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg1017171887	C -> A	LOC_Os10g32780.1	downstream_gene_variant ; 4737.0bp to feature; MODIFIER	silent_mutation	Average:57.128; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg1017171887	C -> A	LOC_Os10g32790-LOC_Os10g32800	intergenic_region ; MODIFIER	silent_mutation	Average:57.128; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg1017171887	C -> DEL	N	N	silent_mutation	Average:57.128; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1017171887	NA	8.39E-06	mr1289	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
vg1017171887	NA	4.85E-06	mr1387	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
vg1017171887	NA	7.30E-07	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
vg1017171887	2.48E-06	2.47E-06	mr1694	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