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Detailed information for vg0724693961:

Variant ID: vg0724693961 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24693961
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:

TAATGTCATGTGGGTAAAGTGTGCCCCCTCTGCAGAGGTTAACAAAATGTTCGAACAGCCATGCCCACGATCATGGGCGGATGTAAGGTGATTCCTTAGC[G/A]
TAGTTTTGTTCGACTACTGCTTTGTGAAATTGCTGTTGGGAATTTGGGTTCGATGTTTGGAACATCAATAGCTGACGGGATCAGCTAGGCCTGGGTGGCC

Reverse complement sequence

GGCCACCCAGGCCTAGCTGATCCCGTCAGCTATTGATGTTCCAAACATCGAACCCAAATTCCCAACAGCAATTTCACAAAGCAGTAGTCGAACAAAACTA[C/T]
GCTAAGGAATCACCTTACATCCGCCCATGATCGTGGGCATGGCTGTTCGAACATTTTGTTAACCTCTGCAGAGGGGGCACACTTTACCCACATGACATTA

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	79.10%	20.60%	0.23%	0.00%	NA
All Indica	2759	66.10%	33.50%	0.36%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	96.30%	3.70%	0.00%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	46.90%	52.30%	0.86%	0.00%	NA
Indica III	913	51.50%	47.90%	0.66%	0.00%	NA
Indica Intermediate	786	69.50%	30.50%	0.00%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	79.20%	20.80%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	1.11%	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
vg0724693961	G -> A	LOC_Os07g41220-LOC_Os07g41230	intergenic_region ; MODIFIER	silent_mutation	Average:31.724; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724693961	NA	2.96E-07	mr1120	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
vg0724693961	3.89E-06	NA	mr1868	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
vg0724693961	NA	4.45E-07	mr1120_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