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Detailed information for vg0434561028:

Variant ID: vg0434561028 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 34561028
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CATATTAATTTTTACAAAATCTCAGATCTACAATTCAACGACATCTGAGGAGATGTGTTCCATATCAAAATTGTAGAGCTCAATGGGATCTACCACTTTG[C/T]
AGTTTATAACATTTGTATTTGAAAGCATTTAAAGTACAATACAAACATTACAAGTTTCGAAGATGTGAAGTAAAATAAACAAAATCTCCAATTTATACAA

Reverse complement sequence

TTGTATAAATTGGAGATTTTGTTTATTTTACTTCACATCTTCGAAACTTGTAATGTTTGTATTGTACTTTAAATGCTTTCAAATACAAATGTTATAAACT[G/A]
CAAAGTGGTAGATCCCATTGAGCTCTACAATTTTGATATGGAACACATCTCCTCAGATGTCGTTGAATTGTAGATCTGAGATTTTGTAAAAATTAATATG

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	84.40%	13.90%	1.71%	0.00%	NA
All Indica	2759	99.10%	0.60%	0.36%	0.00%	NA
All Japonica	1512	55.60%	40.40%	4.03%	0.00%	NA
Aus	269	95.50%	2.60%	1.86%	0.00%	NA
Indica I	595	99.20%	0.50%	0.34%	0.00%	NA
Indica II	465	98.30%	1.10%	0.65%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.00%	0.64%	0.00%	NA
Temperate Japonica	767	25.20%	68.30%	6.52%	0.00%	NA
Tropical Japonica	504	94.60%	4.00%	1.39%	0.00%	NA
Japonica Intermediate	241	70.50%	27.80%	1.66%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	75.60%	18.90%	5.56%	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
vg0434561028	C -> T	LOC_Os04g58020.1	upstream_gene_variant ; 1469.0bp to feature; MODIFIER	silent_mutation	Average:28.327; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0434561028	C -> T	LOC_Os04g58030.1	downstream_gene_variant ; 3356.0bp to feature; MODIFIER	silent_mutation	Average:28.327; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0434561028	C -> T	LOC_Os04g58020-LOC_Os04g58030	intergenic_region ; MODIFIER	silent_mutation	Average:28.327; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0434561028	NA	9.42E-09	mr1866	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
vg0434561028	5.26E-06	NA	mr1449_2	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
vg0434561028	NA	6.43E-09	mr1449_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