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Detailed information for vg0326900441:

Variant ID: vg0326900441 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 26900441
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TTAGATTCTTGTAAATCACTATAAGTGATACAAATTTTAAAATCATGAAAGTACTCCCTAACAGTTTTGTCACCTTGTTTTAGATGTTCTAATTTCTCAA[G/A]
GAGAGTACGTTTATAATATGAAAACACAAAATTTTTTCTCATCATTGTTTTGCATTCATCCCAAGTTTCAAGCTTATGGCCAATAGTATACCACCAAAAA

Reverse complement sequence

TTTTTGGTGGTATACTATTGGCCATAAGCTTGAAACTTGGGATGAATGCAAAACAATGATGAGAAAAAATTTTGTGTTTTCATATTATAAACGTACTCTC[C/T]
TTGAGAAATTAGAACATCTAAAACAAGGTGACAAAACTGTTAGGGAGTACTTTCATGATTTTAAAATTTGTATCACTTATAGTGATTTACAAGAATCTAA

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	41.70%	3.80%	13.48%	41.01%	NA
All Indica	2759	11.90%	6.30%	20.66%	61.11%	NA
All Japonica	1512	98.90%	0.00%	0.00%	1.12%	NA
Aus	269	5.20%	1.50%	18.96%	74.35%	NA
Indica I	595	17.80%	1.00%	10.25%	70.92%	NA
Indica II	465	8.20%	9.50%	27.96%	54.41%	NA
Indica III	913	8.70%	8.10%	24.64%	58.60%	NA
Indica Intermediate	786	13.50%	6.40%	19.59%	60.56%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	98.20%	0.00%	0.00%	1.79%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	87.50%	1.00%	3.12%	8.33%	NA
Intermediate	90	54.40%	1.10%	14.44%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0326900441	G -> A	LOC_Os03g47570.1	missense_variant ; p.Leu279Phe; MODERATE	nonsynonymous_codon ; L279F	Average:7.746; most accessible tissue: Callus, score: 30.414	benign	0.556	TOLERATED	0.29
vg0326900441	G -> DEL	LOC_Os03g47570.1	N	frameshift_variant	Average:7.746; most accessible tissue: Callus, score: 30.414	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0326900441	3.63E-06	3.63E-06	mr1664	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
vg0326900441	NA	1.15E-06	mr1917	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