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Detailed information for vg0817398694:

Variant ID: vg0817398694 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17398694
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTAACATGATTTCTGCTAAAAAAGTTAAAACAACCTCATGATGTTTTGGATTGCTCAACATGTAATTTGAATAAGTTGAAATTGAAAGATTCTTTAGGT[T/C]
GTGTTGAGTACATGGAAGATGTTGTGAAAAACAATGAAGTGCTTTATTGCACCAAATGTCGTAAAAGCAAAGGTGTCATGGTGATTGTGAAAATTGTGCT

Reverse complement sequence

AGCACAATTTTCACAATCACCATGACACCTTTGCTTTTACGACATTTGGTGCAATAAAGCACTTCATTGTTTTTCACAACATCTTCCATGTACTCAACAC[A/G]
ACCTAAAGAATCTTTCAATTTCAACTTATTCAAATTACATGTTGAGCAATCCAAAACATCATGAGGTTGTTTTAACTTTTTTAGCAGAAATCATGTTAAA

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	44.80%	10.50%	1.69%	43.04%	NA
All Indica	2759	18.80%	7.50%	2.79%	70.93%	NA
All Japonica	1512	96.00%	1.60%	0.07%	2.31%	NA
Aus	269	1.50%	91.80%	0.00%	6.69%	NA
Indica I	595	38.70%	0.50%	1.68%	59.16%	NA
Indica II	465	8.00%	9.00%	1.72%	81.29%	NA
Indica III	913	15.80%	7.40%	3.29%	73.49%	NA
Indica Intermediate	786	13.70%	11.80%	3.69%	70.74%	NA
Temperate Japonica	767	99.10%	0.30%	0.00%	0.65%	NA
Tropical Japonica	504	91.10%	3.20%	0.20%	5.56%	NA
Japonica Intermediate	241	96.70%	2.50%	0.00%	0.83%	NA
VI/Aromatic	96	92.70%	6.20%	0.00%	1.04%	NA
Intermediate	90	57.80%	14.40%	2.22%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817398694	T -> C	LOC_Os08g28500.1	intron_variant ; MODIFIER	silent_mutation	Average:10.4; most accessible tissue: Zhenshan97 flag leaf, score: 24.95	N	N	N	N
vg0817398694	T -> DEL	N	N	silent_mutation	Average:10.4; most accessible tissue: Zhenshan97 flag leaf, score: 24.95	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817398694	NA	9.50E-06	mr1374	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
vg0817398694	2.24E-06	NA	mr1632	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