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Detailed information for vg0432569098:

Variant ID: vg0432569098 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32569098
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CTCAACCCGAAAGCAATAACTCGTCGAAATAAAACGAAAGCAAAAAGAGTGGCGATGCGCCGAAATTGTATTGAACGTGTGTGTTAATCATTACATAGGG[C/T]
TCGGGGTCTATTTATACACAAGAAATACAAGATATGTCCATATTGGACACGATTCTTATCTCTAACAAACTCTAAGATACCACAAGTCTTTGCAGCAGAC

Reverse complement sequence

GTCTGCTGCAAAGACTTGTGGTATCTTAGAGTTTGTTAGAGATAAGAATCGTGTCCAATATGGACATATCTTGTATTTCTTGTGTATAAATAGACCCCGA[G/A]
CCCTATGTAATGATTAACACACACGTTCAATACAATTTCGGCGCATCGCCACTCTTTTTGCTTTCGTTTTATTTCGACGAGTTATTGCTTTCGGGTTGAG

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	76.40%	17.50%	5.99%	0.02%	NA
All Indica	2759	77.90%	13.50%	8.55%	0.04%	NA
All Japonica	1512	80.00%	19.30%	0.73%	0.00%	NA
Aus	269	37.50%	49.80%	12.64%	0.00%	NA
Indica I	595	92.40%	5.00%	2.52%	0.00%	NA
Indica II	465	78.70%	12.00%	9.25%	0.00%	NA
Indica III	913	63.00%	22.70%	14.24%	0.11%	NA
Indica Intermediate	786	83.80%	10.10%	6.11%	0.00%	NA
Temperate Japonica	767	93.20%	6.80%	0.00%	0.00%	NA
Tropical Japonica	504	75.20%	23.00%	1.79%	0.00%	NA
Japonica Intermediate	241	47.70%	51.50%	0.83%	0.00%	NA
VI/Aromatic	96	79.20%	19.80%	1.04%	0.00%	NA
Intermediate	90	85.60%	13.30%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0432569098	C -> DEL	N	N	silent_mutation	Average:24.404; most accessible tissue: Zhenshan97 flag leaf, score: 40.929	N	N	N	N
vg0432569098	C -> T	LOC_Os04g54759.1	upstream_gene_variant ; 3693.0bp to feature; MODIFIER	silent_mutation	Average:24.404; most accessible tissue: Zhenshan97 flag leaf, score: 40.929	N	N	N	N
vg0432569098	C -> T	LOC_Os04g54780.1	upstream_gene_variant ; 648.0bp to feature; MODIFIER	silent_mutation	Average:24.404; most accessible tissue: Zhenshan97 flag leaf, score: 40.929	N	N	N	N
vg0432569098	C -> T	LOC_Os04g54759-LOC_Os04g54780	intergenic_region ; MODIFIER	silent_mutation	Average:24.404; most accessible tissue: Zhenshan97 flag leaf, score: 40.929	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432569098	2.92E-06	NA	mr1241_2	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
vg0432569098	NA	2.65E-06	mr1519_2	Jap_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
vg0432569098	2.13E-07	1.24E-09	mr1800_2	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