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Detailed information for vg0504932244:

Variant ID: vg0504932244 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 4932244
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTGTGAAATGATATTTGAAAACTCAGCTTTACGCAAAGTAACCATAGCCACTCCTTGTATTATCCTGTACATTACTGCATTTTGTGTGGTGGCTTGCT[A/G]
AGTACTTTTGTACGCATTGTTGCTCTATATATATCTTTTAGCAGAGTGTTGAAGAGAAACCCTTGTTAGTACGCTTGCGTACCTAACAAGATGATCGGAG

Reverse complement sequence

CTCCGATCATCTTGTTAGGTACGCAAGCGTACTAACAAGGGTTTCTCTTCAACACTCTGCTAAAAGATATATATAGAGCAACAATGCGTACAAAAGTACT[T/C]
AGCAAGCCACCACACAAAATGCAGTAATGTACAGGATAATACAAGGAGTGGCTATGGTTACTTTGCGTAAAGCTGAGTTTTCAAATATCATTTCACAAAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.20%	0.50%	0.28%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	97.60%	1.70%	0.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	97.10%	1.30%	1.56%	0.00%	NA
Tropical Japonica	504	97.00%	3.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0504932244	A -> G	LOC_Os05g08900.1	downstream_gene_variant ; 4069.0bp to feature; MODIFIER	silent_mutation	Average:25.474; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0504932244	A -> G	LOC_Os05g08910.1	downstream_gene_variant ; 2323.0bp to feature; MODIFIER	silent_mutation	Average:25.474; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0504932244	A -> G	LOC_Os05g08920.1	downstream_gene_variant ; 4382.0bp to feature; MODIFIER	silent_mutation	Average:25.474; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0504932244	A -> G	LOC_Os05g08900-LOC_Os05g08910	intergenic_region ; MODIFIER	silent_mutation	Average:25.474; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0504932244	4.96E-09	1.48E-08	mr1546_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