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Detailed information for vg0817111260:

Variant ID: vg0817111260 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17111260
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 46. )

Flanking Sequence (100 bp) in Reference Genome:

CCCTTTTGTGAGTTCGGCTGGGGGAAAGATCTCGCCTCTAGAGTTCGCGTGTCCGCCCTGAAGGCTGCTAGGTAGCGTGTGCGCGACAAGATTATACAGG[T/C]
TTACTGAGAGTCGTCCCCTTGCTCGGTGGGCAGGGTCCTCCTTTTATAGCTCAAGGGGATACCACATGCACCGCCTCTACCTACTCTTCTACGGGGTGGG

Reverse complement sequence

CCCACCCCGTAGAAGAGTAGGTAGAGGCGGTGCATGTGGTATCCCCTTGAGCTATAAAAGGAGGACCCTGCCCACCGAGCAAGGGGACGACTCTCAGTAA[A/G]
CCTGTATAATCTTGTCGCGCACACGCTACCTAGCAGCCTTCAGGGCGGACACGCGAACTCTAGAGGCGAGATCTTTCCCCCAGCCGAACTCACAAAAGGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.80%	17.10%	44.99%	6.12%	NA
All Indica	2759	19.60%	19.40%	55.13%	5.94%	NA
All Japonica	1512	55.90%	10.20%	27.51%	6.42%	NA
Aus	269	19.70%	30.10%	46.47%	3.72%	NA
Indica I	595	10.90%	9.90%	74.79%	4.37%	NA
Indica II	465	14.40%	22.40%	55.70%	7.53%	NA
Indica III	913	31.80%	21.40%	40.42%	6.46%	NA
Indica Intermediate	786	15.00%	22.40%	57.00%	5.60%	NA
Temperate Japonica	767	73.90%	2.70%	19.95%	3.39%	NA
Tropical Japonica	504	31.50%	21.20%	36.11%	11.11%	NA
Japonica Intermediate	241	49.40%	10.80%	33.61%	6.22%	NA
VI/Aromatic	96	28.10%	19.80%	36.46%	15.62%	NA
Intermediate	90	42.20%	22.20%	32.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817111260	T -> C	LOC_Os08g28060.1	upstream_gene_variant ; 3962.0bp to feature; MODIFIER	silent_mutation	Average:63.488; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N
vg0817111260	T -> C	LOC_Os08g28070.1	intron_variant ; MODIFIER	silent_mutation	Average:63.488; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N
vg0817111260	T -> DEL	N	N	silent_mutation	Average:63.488; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817111260	2.85E-06	NA	mr1712	Jap_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