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Detailed information for vg0825168532:

Variant ID: vg0825168532 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25168532
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTCGTTCTCGGTGTGAGGACCGTAGAGATGGGACGTAGTCGAGAACATCATGTGAAGCCCAACGGTCACGAGTGAATTTAAACTGAAGTCCAAAAAAC[C/T]
GCCGCGCGTAACGGACCCAGAAATCTCCGGCGGGCATCTCTCCCCTTTCCTTGGAATTCGCACCGTCGGTAGTGCGTCCATTTAAAGGAATTTTGAGGAT

Reverse complement sequence

ATCCTCAAAATTCCTTTAAATGGACGCACTACCGACGGTGCGAATTCCAAGGAAAGGGGAGAGATGCCCGCCGGAGATTTCTGGGTCCGTTACGCGCGGC[G/A]
GTTTTTTGGACTTCAGTTTAAATTCACTCGTGACCGTTGGGCTTCACATGATGTTCTCGACTACGTCCCATCTCTACGGTCCTCACACCGAGAACGACAA

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	92.90%	0.10%	0.66%	6.39%	NA
All Indica	2759	92.00%	0.10%	0.43%	7.50%	NA
All Japonica	1512	93.60%	0.10%	0.86%	5.49%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	93.10%	0.00%	1.18%	5.71%	NA
Indica II	465	92.70%	0.00%	0.43%	6.88%	NA
Indica III	913	90.10%	0.20%	0.11%	9.53%	NA
Indica Intermediate	786	92.70%	0.10%	0.25%	6.87%	NA
Temperate Japonica	767	99.60%	0.10%	0.13%	0.13%	NA
Tropical Japonica	504	86.50%	0.00%	1.39%	12.10%	NA
Japonica Intermediate	241	89.20%	0.00%	2.07%	8.71%	NA
VI/Aromatic	96	86.50%	0.00%	6.25%	7.29%	NA
Intermediate	90	95.60%	0.00%	0.00%	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
vg0825168532	C -> T	LOC_Os08g39750.1	upstream_gene_variant ; 226.0bp to feature; MODIFIER	silent_mutation	Average:45.588; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0825168532	C -> T	LOC_Os08g39760.1	downstream_gene_variant ; 4268.0bp to feature; MODIFIER	silent_mutation	Average:45.588; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0825168532	C -> T	LOC_Os08g39740-LOC_Os08g39750	intergenic_region ; MODIFIER	silent_mutation	Average:45.588; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0825168532	C -> DEL	N	N	silent_mutation	Average:45.588; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825168532	4.43E-06	NA	mr1110	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