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Detailed information for vg0406265203:

Variant ID: vg0406265203 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6265203
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGATTGGGAATATAACACGTGGCAGTTTAAGAAAGCAAATAAAAAGAACATGGACAGTTGATCGGAAGAGGCAAAGCAAGAACTGGAGAAGTGGAAAA[G/T]
TAAACCATGTCAATGAAGAATTTATAGTGGGGCGAGCTAGGTCAATGGTTTCCGAAGATGAGGTGCTTGGATCTCGGAAATGCTGTTCTGCGATCGATCG

Reverse complement sequence

CGATCGATCGCAGAACAGCATTTCCGAGATCCAAGCACCTCATCTTCGGAAACCATTGACCTAGCTCGCCCCACTATAAATTCTTCATTGACATGGTTTA[C/A]
TTTTCCACTTCTCCAGTTCTTGCTTTGCCTCTTCCGATCAACTGTCCATGTTCTTTTTATTTGCTTTCTTAAACTGCCACGTGTTATATTCCCAATCTTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.40%	10.00%	0.55%	0.02%	NA
All Indica	2759	83.10%	16.80%	0.07%	0.00%	NA
All Japonica	1512	98.10%	0.30%	1.59%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	82.90%	17.10%	0.00%	0.00%	NA
Indica II	465	86.90%	13.10%	0.00%	0.00%	NA
Indica III	913	86.40%	13.50%	0.11%	0.00%	NA
Indica Intermediate	786	77.40%	22.50%	0.13%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	95.60%	0.60%	3.57%	0.20%	NA
Japonica Intermediate	241	97.50%	0.00%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg0406265203	G -> DEL	N	N	silent_mutation	Average:55.742; most accessible tissue: Minghui63 panicle, score: 84.005	N	N	N	N
vg0406265203	G -> T	LOC_Os04g11450.1	upstream_gene_variant ; 1141.0bp to feature; MODIFIER	silent_mutation	Average:55.742; most accessible tissue: Minghui63 panicle, score: 84.005	N	N	N	N
vg0406265203	G -> T	LOC_Os04g11450-LOC_Os04g11470	intergenic_region ; MODIFIER	silent_mutation	Average:55.742; most accessible tissue: Minghui63 panicle, score: 84.005	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406265203	4.36E-06	NA	mr1846	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
vg0406265203	NA	9.16E-09	mr1846	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
vg0406265203	NA	2.04E-06	mr1608_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
vg0406265203	NA	7.13E-06	mr1818_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