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Detailed information for vg0918726676:

Variant ID: vg0918726676 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 18726676
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTGGACAACATCATCTACTTTCCTTCAAGTGAAGCATCTGCAACAGCTATAACATCAATTTGATGGATTATTGTCACTGACATCATCACCAACACCTCT[G/A]
CTTCATCGGCCCTGACATCAACTCTGTTGCTAATGGATAACTATGTCTTCGCCGACTTATTATTTCACTTTCACGGTTGCTATCGACTGGATCACCGACA

Reverse complement sequence

TGTCGGTGATCCAGTCGATAGCAACCGTGAAAGTGAAATAATAAGTCGGCGAAGACATAGTTATCCATTAGCAACAGAGTTGATGTCAGGGCCGATGAAG[C/T]
AGAGGTGTTGGTGATGATGTCAGTGACAATAATCCATCAAATTGATGTTATAGCTGTTGCAGATGCTTCACTTGAAGGAAAGTAGATGATGTTGTCCAAC

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	71.90%	7.30%	20.76%	0.00%	NA
All Indica	2759	54.80%	11.10%	34.14%	0.00%	NA
All Japonica	1512	99.70%	0.10%	0.13%	0.00%	NA
Aus	269	74.70%	14.10%	11.15%	0.00%	NA
Indica I	595	45.00%	8.20%	46.72%	0.00%	NA
Indica II	465	41.30%	12.70%	46.02%	0.00%	NA
Indica III	913	67.50%	11.80%	20.70%	0.00%	NA
Indica Intermediate	786	55.50%	11.30%	33.21%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	0.00%	7.78%	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
vg0918726676	G -> A	LOC_Os09g31130-LOC_Os09g31140	intergenic_region ; MODIFIER	silent_mutation	Average:22.456; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0918726676	3.97E-06	NA	mr1500	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
vg0918726676	NA	3.64E-08	mr1004_2	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