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Detailed information for vg0522746678:

Variant ID: vg0522746678 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 22746678
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: 327. )

Flanking Sequence (100 bp) in Reference Genome:

TGTCGTGGTGGAGCCGGCTGAGCTTCGAGACCTCGTCCAGGAACTCATTGTTGCCTTGGAAGCCATGCCTGTCCAGCTGCTTGATGACCACGGTCTGATC[A/G]
TGCACAAAAAAACAAAGAAAAAACATAATTAGTTCTTGTTTATGCGAAGTGATCACTGCGCTGCTCGATGAAATAGATGTGAGATTGTTGGTGAGCACGT

Reverse complement sequence

ACGTGCTCACCAACAATCTCACATCTATTTCATCGAGCAGCGCAGTGATCACTTCGCATAAACAAGAACTAATTATGTTTTTTCTTTGTTTTTTTGTGCA[T/C]
GATCAGACCGTGGTCATCAAGCAGCTGGACAGGCATGGCTTCCAAGGCAACAATGAGTTCCTGGACGAGGTCTCGAAGCTCAGCCGGCTCCACCACGACA

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	94.60%	5.40%	0.00%	0.00%	NA
All Indica	2759	90.90%	9.10%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	67.70%	32.30%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	98.70%	1.30%	0.00%	0.00%	NA
Indica Intermediate	786	94.70%	5.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	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	96.70%	3.30%	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
vg0522746678	A -> G	LOC_Os05g38770.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:59.349; most accessible tissue: Callus, score: 76.633	N	N	N	N
vg0522746678	A -> G	LOC_Os05g38760.1	upstream_gene_variant ; 2226.0bp to feature; MODIFIER	silent_mutation	Average:59.349; most accessible tissue: Callus, score: 76.633	N	N	N	N
vg0522746678	A -> G	LOC_Os05g38780.1	upstream_gene_variant ; 4865.0bp to feature; MODIFIER	silent_mutation	Average:59.349; most accessible tissue: Callus, score: 76.633	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0522746678	NA	6.52E-06	mr1547	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