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Detailed information for vg0827777299:

Variant ID: vg0827777299 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 27777299
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGGATAACCCGGCGACGGCATTGGATAAGGCCCCCATGACATGTCTTGAGGACGATGATATGTTGGTGATTCCGACCGTCTTGGTGAATGACCAAATC[A/G]
CTCCCTAGGAGGTGATCTTGGTCTTTTCCCTTTATTGCCAGCTTTCTCACCACCTTGCTTCTCATACTTGTCCAAAAGCATATCGAAGGTCACCTTAGTC

Reverse complement sequence

GACTAAGGTGACCTTCGATATGCTTTTGGACAAGTATGAGAAGCAAGGTGGTGAGAAAGCTGGCAATAAAGGGAAAAGACCAAGATCACCTCCTAGGGAG[T/C]
GATTTGGTCATTCACCAAGACGGTCGGAATCACCAACATATCATCGTCCTCAAGACATGTCATGGGGGCCTTATCCAATGCCGTCGCCGGGTTATCCTTT

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	93.70%	5.20%	1.14%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	80.50%	16.00%	3.51%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	64.50%	30.10%	5.35%	0.00%	NA
Tropical Japonica	504	98.80%	0.40%	0.79%	0.00%	NA
Japonica Intermediate	241	92.90%	3.70%	3.32%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0827777299	A -> G	LOC_Os08g44124.1	downstream_gene_variant ; 4829.0bp to feature; MODIFIER	silent_mutation	Average:47.351; most accessible tissue: Callus, score: 58.495	N	N	N	N
vg0827777299	A -> G	LOC_Os08g44110.1	intron_variant ; MODIFIER	silent_mutation	Average:47.351; most accessible tissue: Callus, score: 58.495	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0827777299	4.94E-06	NA	mr1381_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