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Detailed information for vg0508305126:

Variant ID: vg0508305126 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 8305126
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

AATTAAAATGTTACTAATCCAACCAAGACAATGTAATCTCTTCAGTAAAATTGTGCTTAAGCAGCTGTGAGATTTGAGCCTAAATGATATCTCGAGTTAA[A/G]
TCTTGTTACTTATTTTCAAGTATTATACCACAAGAGGGAGAAGCAAAAGCCTCACCTCATGGAGAGAGGAGCGGCGTGGCTACATTCACTATGAAAGGCT

Reverse complement sequence

AGCCTTTCATAGTGAATGTAGCCACGCCGCTCCTCTCTCCATGAGGTGAGGCTTTTGCTTCTCCCTCTTGTGGTATAATACTTGAAAATAAGTAACAAGA[T/C]
TTAACTCGAGATATCATTTAGGCTCAAATCTCACAGCTGCTTAAGCACAATTTTACTGAAGAGATTACATTGTCTTGGTTGGATTAGTAACATTTTAATT

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	97.30%	2.20%	0.55%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.11%	0.00%	NA
All Japonica	1512	91.90%	6.70%	1.46%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	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	96.00%	2.20%	1.83%	0.00%	NA
Tropical Japonica	504	88.30%	11.30%	0.40%	0.00%	NA
Japonica Intermediate	241	86.30%	11.20%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0508305126	A -> G	LOC_Os05g14570.1	downstream_gene_variant ; 1858.0bp to feature; MODIFIER	silent_mutation	Average:32.115; most accessible tissue: Zhenshan97 young leaf, score: 46.636	N	N	N	N
vg0508305126	A -> G	LOC_Os05g14580.1	intron_variant ; MODIFIER	silent_mutation	Average:32.115; most accessible tissue: Zhenshan97 young leaf, score: 46.636	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0508305126	1.75E-06	1.75E-06	mr1577	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
vg0508305126	NA	1.07E-07	mr1549_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251