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Detailed information for vg0906245690:

Variant ID: vg0906245690 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6245690
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, A: 0.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAGTAACCAACGCTCAGACAACAGACTGAAGAGAAAAGCCTTTTAACCGCCCAGTCCTTTGATGATGAGAACGTACGTGGTCATGCGAGGCCACTCAT[G/A]
TAATCTTATTAGCATCTATCTCCTAGCTCTTAGCTTGTGTTAGGCATTAGCAATTGTGTATTGTAGTCCAGAACAATGCATTAGCCAGTTGTAGTCTTAT

Reverse complement sequence

ATAAGACTACAACTGGCTAATGCATTGTTCTGGACTACAATACACAATTGCTAATGCCTAACACAAGCTAAGAGCTAGGAGATAGATGCTAATAAGATTA[C/T]
ATGAGTGGCCTCGCATGACCACGTACGTTCTCATCATCAAAGGACTGGGCGGTTAAAAGGCTTTTCTCTTCAGTCTGTTGTCTGAGCGTTGGTTACTTCC

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	91.10%	8.90%	0.06%	0.00%	NA
All Indica	2759	88.90%	11.00%	0.07%	0.00%	NA
All Japonica	1512	94.40%	5.60%	0.00%	0.00%	NA
Aus	269	93.70%	6.30%	0.00%	0.00%	NA
Indica I	595	79.80%	20.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	91.90%	8.00%	0.11%	0.00%	NA
Indica Intermediate	786	86.00%	13.90%	0.13%	0.00%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	89.70%	10.30%	0.00%	0.00%	NA
Japonica Intermediate	241	90.00%	10.00%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	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
vg0906245690	G -> A	LOC_Os09g11240.1	3_prime_UTR_variant ; 53.0bp to feature; MODIFIER	silent_mutation	Average:78.879; most accessible tissue: Callus, score: 94.446	N	N	N	N
vg0906245690	G -> A	LOC_Os09g11250.1	downstream_gene_variant ; 547.0bp to feature; MODIFIER	silent_mutation	Average:78.879; most accessible tissue: Callus, score: 94.446	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906245690	1.11E-06	1.11E-06	mr1193_2	Jap_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