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Detailed information for vg0112525480:

Variant ID: vg0112525480 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12525480
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGACCAGTACTGATACAGAACGTGGATCAACTTCAGAAGTCACTGCTCCTTTGCACATTCAACGACAACATCCGCCGGAATAAATCATTGGTAATATAG[G/A]
TGAGCGGACTACAAGGTCTAAGGTAACGACTCATGATGTTTGTGCAAATTCTGCATTTGTTGCTTCTTTTGAACCCAAAGATGTGTCACATGCATTAACT

Reverse complement sequence

AGTTAATGCATGTGACACATCTTTGGGTTCAAAAGAAGCAACAAATGCAGAATTTGCACAAACATCATGAGTCGTTACCTTAGACCTTGTAGTCCGCTCA[C/T]
CTATATTACCAATGATTTATTCCGGCGGATGTTGTCGTTGAATGTGCAAAGGAGCAGTGACTTCTGAAGTTGATCCACGTTCTGTATCAGTACTGGTCGA

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	96.00%	4.00%	0.02%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	88.00%	12.00%	0.07%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	91.50%	8.50%	0.00%	0.00%	NA
Tropical Japonica	504	85.30%	14.50%	0.20%	0.00%	NA
Japonica Intermediate	241	82.20%	17.80%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0112525480	G -> A	LOC_Os01g22270.1	missense_variant&splice_region_variant ; p.Gly893Asp; MODERATE	nonsynonymous_codon ; G893D	Average:24.715; most accessible tissue: Zhenshan97 flag leaf, score: 51.466	unknown	unknown	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112525480	2.23E-06	NA	mr1889	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