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Detailed information for vg0324153872:

Variant ID: vg0324153872 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24153872
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATTATTTGAATTTCTTATATTTTAAAATTCAAATTTTGTATAGTCCAATCAAACTCGGATGGAGAAATGACCAAAATAAAATTGGTAGATCTCAATGA[G/A]
TTCTACAACTTTGTTTTTGACAACTTTTTGACATGAGTTGATTTAATGTCATAAAAATCAATTTAAAGTTTAAAAAACACATGATTTTTGCATGCGGACG

Reverse complement sequence

CGTCCGCATGCAAAAATCATGTGTTTTTTAAACTTTAAATTGATTTTTATGACATTAAATCAACTCATGTCAAAAAGTTGTCAAAAACAAAGTTGTAGAA[C/T]
TCATTGAGATCTACCAATTTTATTTTGGTCATTTCTCCATCCGAGTTTGATTGGACTATACAAAATTTGAATTTTAAAATATAAGAAATTCAAATAATTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.60%	1.60%	2.62%	24.16%	NA
All Indica	2759	53.20%	2.70%	4.39%	39.69%	NA
All Japonica	1512	99.50%	0.00%	0.00%	0.46%	NA
Aus	269	94.10%	0.00%	0.00%	5.95%	NA
Indica I	595	39.20%	0.00%	2.18%	58.66%	NA
Indica II	465	44.50%	0.00%	3.23%	52.26%	NA
Indica III	913	69.10%	7.20%	7.45%	16.21%	NA
Indica Intermediate	786	50.60%	1.00%	3.18%	45.17%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	92.70%	3.10%	3.12%	1.04%	NA
Intermediate	90	74.40%	0.00%	0.00%	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
vg0324153872	G -> A	LOC_Os03g43330.1	upstream_gene_variant ; 523.0bp to feature; MODIFIER	silent_mutation	Average:28.822; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0324153872	G -> A	LOC_Os03g43309-LOC_Os03g43330	intergenic_region ; MODIFIER	silent_mutation	Average:28.822; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0324153872	G -> DEL	N	N	silent_mutation	Average:28.822; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324153872	3.77E-08	3.77E-08	mr1341_2	Ind_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