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Detailed information for vg0905898979:

Variant ID: vg0905898979 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5898979
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.52, G: 0.48, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

TGCGGGCGAGGCGGCTTGGCCGGTGGCCGGCGCTTTCTAGCGGCCGATGCAGCCATGTAGGTGAGGCCGTCGCCTAGCAGGTGCAGCTGATACCAAGTGC[A/G]
GTCGGCGCGTGATGTGACCATGGCTACTACGGATACAACCGTTGCTCACATCATGGATGAACAAGAAGATATGAATATAAGATATGAACATCAAGTCCTC

Reverse complement sequence

GAGGACTTGATGTTCATATCTTATATTCATATCTTCTTGTTCATCCATGATGTGAGCAACGGTTGTATCCGTAGTAGCCATGGTCACATCACGCGCCGAC[T/C]
GCACTTGGTATCAGCTGCACCTGCTAGGCGACGGCCTCACCTACATGGCTGCATCGGCCGCTAGAAAGCGCCGGCCACCGGCCAAGCCGCCTCGCCCGCA

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	70.70%	29.30%	0.00%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.00%	0.00%	NA
All Japonica	1512	15.50%	84.50%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	97.70%	2.30%	0.00%	0.00%	NA
Temperate Japonica	767	9.00%	91.00%	0.00%	0.00%	NA
Tropical Japonica	504	17.90%	82.10%	0.00%	0.00%	NA
Japonica Intermediate	241	31.10%	68.90%	0.00%	0.00%	NA
VI/Aromatic	96	71.90%	28.10%	0.00%	0.00%	NA
Intermediate	90	56.70%	43.30%	0.00%	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
vg0905898979	A -> G	LOC_Os09g10800.1	upstream_gene_variant ; 1866.0bp to feature; MODIFIER	silent_mutation	Average:73.548; most accessible tissue: Zhenshan97 young leaf, score: 86.383	N	N	N	N
vg0905898979	A -> G	LOC_Os09g10810.1	upstream_gene_variant ; 20.0bp to feature; MODIFIER	silent_mutation	Average:73.548; most accessible tissue: Zhenshan97 young leaf, score: 86.383	N	N	N	N
vg0905898979	A -> G	LOC_Os09g10820.1	upstream_gene_variant ; 1654.0bp to feature; MODIFIER	silent_mutation	Average:73.548; most accessible tissue: Zhenshan97 young leaf, score: 86.383	N	N	N	N
vg0905898979	A -> G	LOC_Os09g10800-LOC_Os09g10810	intergenic_region ; MODIFIER	silent_mutation	Average:73.548; most accessible tissue: Zhenshan97 young leaf, score: 86.383	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905898979	8.80E-06	8.03E-06	mr1150_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