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Detailed information for vg1001388587:

Variant ID: vg1001388587 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1388587
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.19, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCCAGCTTGATCTATCCATCCTACATCTGCCTATATAAAGCACCTTGACTCCCACTGCTCGGGGGGCTGGCAGATGCATCCATGCAGAAGCGCTAAGG[C/T]
GCTGCACATACACGCCACGCCGGCGCCGCCGACGCTATGCGCTGCGCAGAGATGCAGGCCCTGCGCCGGTGGCCGGCGGCACATGTGCCCACAAATATTT

Reverse complement sequence

AAATATTTGTGGGCACATGTGCCGCCGGCCACCGGCGCAGGGCCTGCATCTCTGCGCAGCGCATAGCGTCGGCGGCGCCGGCGTGGCGTGTATGTGCAGC[G/A]
CCTTAGCGCTTCTGCATGGATGCATCTGCCAGCCCCCCGAGCAGTGGGAGTCAAGGTGCTTTATATAGGCAGATGTAGGATGGATAGATCAAGCTGGCAC

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	71.80%	26.50%	0.68%	1.06%	NA
All Indica	2759	64.70%	32.80%	1.05%	1.52%	NA
All Japonica	1512	94.80%	5.10%	0.07%	0.07%	NA
Aus	269	6.30%	93.70%	0.00%	0.00%	NA
Indica I	595	61.00%	38.00%	0.67%	0.34%	NA
Indica II	465	70.80%	28.60%	0.22%	0.43%	NA
Indica III	913	63.30%	32.40%	1.97%	2.30%	NA
Indica Intermediate	786	65.40%	31.70%	0.76%	2.16%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	86.30%	13.70%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	2.50%	0.41%	0.41%	NA
VI/Aromatic	96	86.50%	5.20%	2.08%	6.25%	NA
Intermediate	90	82.20%	16.70%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001388587	C -> T	LOC_Os10g03270.1	upstream_gene_variant ; 3012.0bp to feature; MODIFIER	silent_mutation	Average:67.11; most accessible tissue: Zhenshan97 flag leaf, score: 84.585	N	N	N	N
vg1001388587	C -> T	LOC_Os10g03280.1	upstream_gene_variant ; 218.0bp to feature; MODIFIER	silent_mutation	Average:67.11; most accessible tissue: Zhenshan97 flag leaf, score: 84.585	N	N	N	N
vg1001388587	C -> T	LOC_Os10g03290.1	upstream_gene_variant ; 2226.0bp to feature; MODIFIER	silent_mutation	Average:67.11; most accessible tissue: Zhenshan97 flag leaf, score: 84.585	N	N	N	N
vg1001388587	C -> T	LOC_Os10g03270-LOC_Os10g03280	intergenic_region ; MODIFIER	silent_mutation	Average:67.11; most accessible tissue: Zhenshan97 flag leaf, score: 84.585	N	N	N	N
vg1001388587	C -> DEL	N	N	silent_mutation	Average:67.11; most accessible tissue: Zhenshan97 flag leaf, score: 84.585	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001388587	8.69E-11	NA	mr1486	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
vg1001388587	1.61E-12	7.62E-15	mr1486	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
vg1001388587	3.39E-08	NA	mr1548	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
vg1001388587	5.06E-09	2.28E-10	mr1548	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
vg1001388587	1.79E-08	NA	mr1721	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
vg1001388587	1.46E-07	2.53E-10	mr1721	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
vg1001388587	3.09E-09	NA	mr1486_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
vg1001388587	2.49E-11	1.67E-14	mr1486_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
vg1001388587	4.36E-11	NA	mr1721_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
vg1001388587	1.18E-09	3.59E-12	mr1721_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