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Detailed information for vg0212092329:

Variant ID: vg0212092329 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 12092329
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTTCACGCCAAAATTGGAAGTTTGGTTGAAATTGGAACGATGTGACGGAAAAGTTGGAAGTTTATGTGTGTAGGAAAGTTTTGATGTGATGGAAAAGTT[G/A]
GAAGTTTGAAGAAAAAGTTTAGAACTAAACTCGGCCAAAGTTTGAATCTAAACAAGGGCCGAGTTTACTTCCAAACTATTTTAACTTTTTTCTTCAAACT

Reverse complement sequence

AGTTTGAAGAAAAAAGTTAAAATAGTTTGGAAGTAAACTCGGCCCTTGTTTAGATTCAAACTTTGGCCGAGTTTAGTTCTAAACTTTTTCTTCAAACTTC[C/T]
AACTTTTCCATCACATCAAAACTTTCCTACACACATAAACTTCCAACTTTTCCGTCACATCGTTCCAATTTCAACCAAACTTCCAATTTTGGCGTGAACT

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	95.80%	4.10%	0.13%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	87.30%	12.30%	0.40%	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	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	96.70%	3.00%	0.26%	0.00%	NA
Tropical Japonica	504	72.40%	27.00%	0.60%	0.00%	NA
Japonica Intermediate	241	88.40%	11.20%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0212092329	G -> A	LOC_Os02g20500.1	upstream_gene_variant ; 1217.0bp to feature; MODIFIER	silent_mutation	Average:23.858; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0212092329	G -> A	LOC_Os02g20490.1	downstream_gene_variant ; 2977.0bp to feature; MODIFIER	silent_mutation	Average:23.858; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0212092329	G -> A	LOC_Os02g20500-LOC_Os02g20510	intergenic_region ; MODIFIER	silent_mutation	Average:23.858; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0212092329	3.20E-06	3.20E-06	mr1362	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