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Detailed information for vg0726576732:

Variant ID: vg0726576732 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 26576732
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTAGTCAACTCAGCATGAAGACAAAATTATGTTCTGATCATGGTTTGAGGATTTCCAATACATACCTGCGGAGGCGGATTGAATGCATTGTATGGCAC[G/A]
ACTGGCAGCTGGTGTGAGTAGCTGACGACGATTGCATTTGAGAAGATTTTATACATCCTCTCCTTCATGATTCTGAAATCCAGAGAGTCTGATTCTTCAC

Reverse complement sequence

GTGAAGAATCAGACTCTCTGGATTTCAGAATCATGAAGGAGAGGATGTATAAAATCTTCTCAAATGCAATCGTCGTCAGCTACTCACACCAGCTGCCAGT[C/T]
GTGCCATACAATGCATTCAATCCGCCTCCGCAGGTATGTATTGGAAATCCTCAAACCATGATCAGAACATAATTTTGTCTTCATGCTGAGTTGACTAACT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.20%	27.60%	16.19%	3.05%	NA
All Indica	2759	69.80%	12.50%	16.17%	1.49%	NA
All Japonica	1512	25.90%	52.20%	15.21%	6.68%	NA
Aus	269	25.70%	49.10%	25.28%	0.00%	NA
Indica I	595	71.30%	9.10%	18.99%	0.67%	NA
Indica II	465	55.30%	18.30%	20.65%	5.81%	NA
Indica III	913	81.60%	7.90%	10.41%	0.11%	NA
Indica Intermediate	786	63.60%	17.20%	18.07%	1.15%	NA
Temperate Japonica	767	2.10%	78.40%	7.43%	12.13%	NA
Tropical Japonica	504	58.70%	18.30%	22.22%	0.79%	NA
Japonica Intermediate	241	32.80%	40.20%	25.31%	1.66%	NA
VI/Aromatic	96	88.50%	5.20%	6.25%	0.00%	NA
Intermediate	90	45.60%	35.60%	16.67%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0726576732	G -> DEL	N	N	silent_mutation	Average:25.24; most accessible tissue: Minghui63 young leaf, score: 40.718	N	N	N	N
vg0726576732	G -> A	LOC_Os07g44499.1	intron_variant ; MODIFIER	silent_mutation	Average:25.24; most accessible tissue: Minghui63 young leaf, score: 40.718	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0726576732	4.59E-06	4.59E-06	mr1303	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