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Detailed information for vg1215306532:

Variant ID: vg1215306532 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15306532
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.55, G: 0.45, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

TTGCACAAATTATTAACACAATCCGAACCATCGCTTGGCTCGGCTATACATAATATTGCACTATCATCTAAACTAACGTTTAAACTATTATCATCCACTC[A/G]
GCTTTCCTGAGCCAGAGCTTCATGCAACATATGATCAACATCAAGAAATATCTGGCCATTCAATTTCTCTTTAATAGAATCAAGCAAAACATCATATGCA

Reverse complement sequence

TGCATATGATGTTTTGCTTGATTCTATTAAAGAGAAATTGAATGGCCAGATATTTCTTGATGTTGATCATATGTTGCATGAAGCTCTGGCTCAGGAAAGC[T/C]
GAGTGGATGATAATAGTTTAAACGTTAGTTTAGATGATAGTGCAATATTATGTATAGCCGAGCCAAGCGATGGTTCGGATTGTGTTAATAATTTGTGCAA

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	43.10%	10.20%	9.69%	37.01%	NA
All Indica	2759	31.60%	4.00%	12.76%	51.69%	NA
All Japonica	1512	71.20%	17.50%	1.92%	9.33%	NA
Aus	269	10.80%	14.90%	19.70%	54.65%	NA
Indica I	595	13.30%	0.70%	16.13%	69.92%	NA
Indica II	465	60.00%	9.90%	9.89%	20.22%	NA
Indica III	913	23.00%	3.80%	14.13%	59.04%	NA
Indica Intermediate	786	38.70%	3.10%	10.31%	47.96%	NA
Temperate Japonica	767	91.90%	4.30%	0.91%	2.87%	NA
Tropical Japonica	504	43.50%	35.70%	1.59%	19.25%	NA
Japonica Intermediate	241	63.50%	21.60%	5.81%	9.13%	NA
VI/Aromatic	96	12.50%	55.20%	18.75%	13.54%	NA
Intermediate	90	52.20%	16.70%	6.67%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215306532	A -> DEL	N	N	silent_mutation	Average:22.047; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1215306532	A -> G	LOC_Os12g26250.1	upstream_gene_variant ; 4257.0bp to feature; MODIFIER	silent_mutation	Average:22.047; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg1215306532	A -> G	LOC_Os12g26260.1	intron_variant ; MODIFIER	silent_mutation	Average:22.047; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215306532	NA	7.46E-07	mr1709	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
vg1215306532	NA	3.76E-11	mr1709	Ind_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
vg1215306532	5.04E-08	NA	mr1022_2	Ind_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
vg1215306532	NA	1.52E-06	mr1558_2	Ind_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