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Detailed information for vg0417517608:

Variant ID: vg0417517608 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17517608
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

CTAAAATAGGGCATGGGTAAACTTCGCTTTCCCATTGGGTTGACCGCTGGTTATGTTAAAATAGTAATGCTAGTGTTGTTTTCTCAGAACCCTACAAATA[T/C]
ACAAATTATGATGCACCTCATGTTGCTGTAGAATAGCTGAAACTCGTAATTTTTTTGGGTATCAAGAACATTCTCTAAAAAAGGGAACCGACAGCTCCTC

Reverse complement sequence

GAGGAGCTGTCGGTTCCCTTTTTTAGAGAATGTTCTTGATACCCAAAAAAATTACGAGTTTCAGCTATTCTACAGCAACATGAGGTGCATCATAATTTGT[A/G]
TATTTGTAGGGTTCTGAGAAAACAACACTAGCATTACTATTTTAACATAACCAGCGGTCAACCCAATGGGAAAGCGAAGTTTACCCATGCCCTATTTTAG

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	63.90%	11.50%	0.70%	23.87%	NA
All Indica	2759	57.20%	5.30%	1.05%	36.46%	NA
All Japonica	1512	74.70%	25.10%	0.20%	0.00%	NA
Aus	269	61.00%	3.70%	0.00%	35.32%	NA
Indica I	595	76.80%	20.80%	0.34%	2.02%	NA
Indica II	465	58.70%	0.20%	1.51%	39.57%	NA
Indica III	913	38.90%	0.70%	1.10%	59.36%	NA
Indica Intermediate	786	62.80%	1.80%	1.27%	34.10%	NA
Temperate Japonica	767	57.40%	42.20%	0.39%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	78.40%	21.60%	0.00%	0.00%	NA
VI/Aromatic	96	78.10%	3.10%	0.00%	18.75%	NA
Intermediate	90	80.00%	8.90%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0417517608	T -> C	LOC_Os04g29450.1	upstream_gene_variant ; 4169.0bp to feature; MODIFIER	silent_mutation	Average:43.172; most accessible tissue: Zhenshan97 flower, score: 88.623	N	N	N	N
vg0417517608	T -> C	LOC_Os04g29469.1	intron_variant ; MODIFIER	silent_mutation	Average:43.172; most accessible tissue: Zhenshan97 flower, score: 88.623	N	N	N	N
vg0417517608	T -> DEL	N	N	silent_mutation	Average:43.172; most accessible tissue: Zhenshan97 flower, score: 88.623	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417517608	4.85E-06	4.77E-06	mr1923_2	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