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Detailed information for vg0728292241:

Variant ID: vg0728292241 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 28292241
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGGGGAAGAAGAAGGCAGAGCAGCGGCGGCAAGGCGAAAATCGGCGCGGCGGTGCGGTTGAGGAGCGGCACCGTGGTGGACTGGTGGGGGTGGGGATC[G/A]
GACTGGGCTGGATATGGGCTCGAAAATATTTGGACGAAATTACCCCTCGCTAATGGTAATTAAGTGCTAATCTCCCTTTTAATCACAGCCACTGATTAGC

Reverse complement sequence

GCTAATCAGTGGCTGTGATTAAAAGGGAGATTAGCACTTAATTACCATTAGCGAGGGGTAATTTCGTCCAAATATTTTCGAGCCCATATCCAGCCCAGTC[C/T]
GATCCCCACCCCCACCAGTCCACCACGGTGCCGCTCCTCAACCGCACCGCCGCGCCGATTTTCGCCTTGCCGCCGCTGCTCTGCCTTCTTCTTCCCCTTG

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	94.90%	3.60%	1.52%	0.00%	NA
All Indica	2759	91.50%	6.00%	2.50%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	88.40%	6.10%	5.55%	0.00%	NA
Indica II	465	94.20%	3.20%	2.58%	0.00%	NA
Indica III	913	90.50%	9.00%	0.55%	0.00%	NA
Indica Intermediate	786	93.40%	4.20%	2.42%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	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
vg0728292241	G -> A	LOC_Os07g47320.1	intron_variant ; MODIFIER	silent_mutation	Average:73.232; most accessible tissue: Zhenshan97 panicle, score: 84.374	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0728292241	8.28E-06	NA	mr1398_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