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Detailed information for vg0910827004:

Variant ID: vg0910827004 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10827004
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTTTGCATAGCAATTTTGAAGAAAAAAAAGTTGAATAAAAGCCACAAAAAGAAACCAAAAAAATCCAGCTCATCGTATAAAATACTCCCAACTGCCTC[G/A]
CTTCCCTTCCCCTCTAGCTTCTACTAGTACTCGTTCTGCACACACGCACACCACCTCTCTCCTCTCCTCTCCTCCCTCCGCGCGTGCGCCTCCAGATTTG

Reverse complement sequence

CAAATCTGGAGGCGCACGCGCGGAGGGAGGAGAGGAGAGGAGAGAGGTGGTGTGCGTGTGTGCAGAACGAGTACTAGTAGAAGCTAGAGGGGAAGGGAAG[C/T]
GAGGCAGTTGGGAGTATTTTATACGATGAGCTGGATTTTTTTGGTTTCTTTTTGTGGCTTTTATTCAACTTTTTTTTCTTCAAAATTGCTATGCAAACAA

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	89.30%	2.80%	0.36%	7.55%	NA
All Indica	2759	87.40%	0.30%	0.54%	11.82%	NA
All Japonica	1512	94.10%	5.90%	0.00%	0.00%	NA
Aus	269	88.10%	1.10%	0.74%	10.04%	NA
Indica I	595	89.20%	0.00%	0.00%	10.76%	NA
Indica II	465	98.10%	0.20%	0.43%	1.29%	NA
Indica III	913	78.60%	0.10%	0.88%	20.37%	NA
Indica Intermediate	786	89.80%	0.60%	0.64%	8.91%	NA
Temperate Japonica	767	95.00%	5.00%	0.00%	0.00%	NA
Tropical Japonica	504	97.20%	2.80%	0.00%	0.00%	NA
Japonica Intermediate	241	84.60%	15.40%	0.00%	0.00%	NA
VI/Aromatic	96	66.70%	32.30%	0.00%	1.04%	NA
Intermediate	90	92.20%	4.40%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910827004	G -> DEL	N	N	silent_mutation	Average:51.994; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N
vg0910827004	G -> A	LOC_Os09g17690.1	upstream_gene_variant ; 4871.0bp to feature; MODIFIER	silent_mutation	Average:51.994; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N
vg0910827004	G -> A	LOC_Os09g17700.1	downstream_gene_variant ; 754.0bp to feature; MODIFIER	silent_mutation	Average:51.994; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N
vg0910827004	G -> A	LOC_Os09g17710.1	downstream_gene_variant ; 3075.0bp to feature; MODIFIER	silent_mutation	Average:51.994; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N
vg0910827004	G -> A	LOC_Os09g17700-LOC_Os09g17710	intergenic_region ; MODIFIER	silent_mutation	Average:51.994; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910827004	1.62E-07	1.62E-07	mr1915	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