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Detailed information for vg0826323144:

Variant ID: vg0826323144 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 26323144
Reference Allele: C	Alternative Allele: T
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: 124. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGGACTTTGTAGGAAAAATTCCTATAAGAATGAAATCCTCTAAAATTCCTATGAATTTCCTTTGAATCAAAGGGGCCTTAATTTTATATCGCCAAGAA[C/T]
ATGTATATAAGTTTTATACACAGATTTTTTTTTTTCATTTGCAAATAGTATATTGTTTCTCTTTTTTCCTTCGATATGATAGGGCTGCATGTTCCCTCTC

Reverse complement sequence

GAGAGGGAACATGCAGCCCTATCATATCGAAGGAAAAAAGAGAAACAATATACTATTTGCAAATGAAAAAAAAAAATCTGTGTATAAAACTTATATACAT[G/A]
TTCTTGGCGATATAAAATTAAGGCCCCTTTGATTCAAAGGAAATTCATAGGAATTTTAGAGGATTTCATTCTTATAGGAATTTTTCCTACAAAGTCCTTT

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	69.10%	11.90%	15.21%	3.72%	NA
All Indica	2759	49.00%	19.90%	25.08%	5.94%	NA
All Japonica	1512	98.90%	0.10%	0.60%	0.33%	NA
Aus	269	96.70%	0.00%	2.23%	1.12%	NA
Indica I	595	56.30%	9.10%	31.26%	3.36%	NA
Indica II	465	34.20%	33.80%	26.02%	6.02%	NA
Indica III	913	56.10%	17.90%	19.06%	7.01%	NA
Indica Intermediate	786	44.10%	22.40%	26.84%	6.62%	NA
Temperate Japonica	767	98.70%	0.10%	0.78%	0.39%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	0.00%	1.24%	0.83%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	71.10%	11.10%	13.33%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0826323144	C -> T	LOC_Os08g41700.1	upstream_gene_variant ; 619.0bp to feature; MODIFIER	silent_mutation	Average:31.272; most accessible tissue: Minghui63 flower, score: 44.843	N	N	N	N
vg0826323144	C -> T	LOC_Os08g41710.1	upstream_gene_variant ; 1852.0bp to feature; MODIFIER	silent_mutation	Average:31.272; most accessible tissue: Minghui63 flower, score: 44.843	N	N	N	N
vg0826323144	C -> T	LOC_Os08g41700-LOC_Os08g41710	intergenic_region ; MODIFIER	silent_mutation	Average:31.272; most accessible tissue: Minghui63 flower, score: 44.843	N	N	N	N
vg0826323144	C -> DEL	N	N	silent_mutation	Average:31.272; most accessible tissue: Minghui63 flower, score: 44.843	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0826323144	NA	1.07E-06	mr1432	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
vg0826323144	NA	3.39E-06	mr1433	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
vg0826323144	NA	1.73E-07	mr1629	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