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Detailed information for vg0900528417:

Variant ID: vg0900528417 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 528417
Reference Allele: A	Alternative Allele: G,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TTGCATATCCATCTTTGAGGTAATCGATACAACACTCGACAATCTCTTCAGTACTATAACCCTCAACCATCGATCCCTCTGGATGTGCACGATTTCGGAC[A/G,C]
TAACCCTTCAAAACTGCCATGTAACGCTCGTATGACCACATTTGATGGAGGTACAATGGGCCAAGCGCAACCATCTACGGCACTATGTGAACAATGAGGT

Reverse complement sequence

ACCTCATTGTTCACATAGTGCCGTAGATGGTTGCGCTTGGCCCATTGTACCTCCATCAAATGTGGTCATACGAGCGTTACATGGCAGTTTTGAAGGGTTA[T/C,G]
GTCCGAAATCGTGCACATCCAGAGGGATCGATGGTTGAGGGTTATAGTACTGAAGAGATTGTCGAGTGTTGTATCGATTACCTCAAAGATGGATATGCAA

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	61.10%	28.80%	5.10%	4.97%	C: 0.04%
All Indica	2759	87.10%	6.30%	6.45%	0.18%	NA
All Japonica	1512	16.00%	67.70%	0.99%	15.21%	C: 0.13%
Aus	269	72.50%	11.50%	15.99%	0.00%	NA
Indica I	595	90.80%	3.00%	5.88%	0.34%	NA
Indica II	465	86.70%	4.10%	9.25%	0.00%	NA
Indica III	913	84.10%	9.60%	6.02%	0.22%	NA
Indica Intermediate	786	87.90%	6.20%	5.73%	0.13%	NA
Temperate Japonica	767	17.70%	51.90%	1.69%	28.42%	C: 0.26%
Tropical Japonica	504	6.90%	92.90%	0.20%	0.00%	NA
Japonica Intermediate	241	29.50%	65.10%	0.41%	4.98%	NA
VI/Aromatic	96	12.50%	86.50%	1.04%	0.00%	NA
Intermediate	90	41.10%	54.40%	4.44%	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
vg0900528417	A -> G	LOC_Os09g01750.1	upstream_gene_variant ; 2801.0bp to feature; MODIFIER	silent_mutation	Average:27.559; most accessible tissue: Zhenshan97 flag leaf, score: 49.845	N	N	N	N
vg0900528417	A -> G	LOC_Os09g01760.1	intron_variant ; MODIFIER	silent_mutation	Average:27.559; most accessible tissue: Zhenshan97 flag leaf, score: 49.845	N	N	N	N
vg0900528417	A -> DEL	N	N	silent_mutation	Average:27.559; most accessible tissue: Zhenshan97 flag leaf, score: 49.845	N	N	N	N
vg0900528417	A -> C	LOC_Os09g01750.1	upstream_gene_variant ; 2801.0bp to feature; MODIFIER	silent_mutation	Average:27.559; most accessible tissue: Zhenshan97 flag leaf, score: 49.845	N	N	N	N
vg0900528417	A -> C	LOC_Os09g01760.1	intron_variant ; MODIFIER	silent_mutation	Average:27.559; most accessible tissue: Zhenshan97 flag leaf, score: 49.845	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900528417	NA	8.47E-09	mr1162	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