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Detailed information for vg1225574338:

Variant ID: vg1225574338 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 25574338
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, T: 0.10, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGCCAGATAGGGAAGAAAAATTTTGAGGGTGTTTGTATAGGGAACTTTTGAAGTTTGGATGCTATAGAGAGAAGAGCAACTTTTTTTATGCTATATA[T/G]
GGAATTTTCTCATTATTGAAAACCTTATGTTCGGGAACCTAGCGTAGGATATAGCCCCCCCTCTTTTTCTTCTAAGGCATTTTCTTAGCTCACATGTTTT

Reverse complement sequence

AAAACATGTGAGCTAAGAAAATGCCTTAGAAGAAAAAGAGGGGGGGCTATATCCTACGCTAGGTTCCCGAACATAAGGTTTTCAATAATGAGAAAATTCC[A/C]
TATATAGCATAAAAAAAGTTGCTCTTCTCTCTATAGCATCCAAACTTCAAAAGTTCCCTATACAAACACCCTCAAAATTTTTCTTCCCTATCTGGCATTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.00%	11.80%	0.32%	7.85%	NA
All Indica	2759	79.10%	14.20%	0.18%	6.52%	NA
All Japonica	1512	96.40%	3.40%	0.13%	0.07%	NA
Aus	269	1.90%	33.10%	2.23%	62.83%	NA
Indica I	595	81.80%	2.90%	0.67%	14.62%	NA
Indica II	465	90.10%	8.20%	0.00%	1.72%	NA
Indica III	913	69.80%	27.60%	0.00%	2.63%	NA
Indica Intermediate	786	81.30%	10.80%	0.13%	7.76%	NA
Temperate Japonica	767	95.20%	4.60%	0.26%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	5.40%	0.00%	0.41%	NA
VI/Aromatic	96	72.90%	13.50%	0.00%	13.54%	NA
Intermediate	90	75.60%	13.30%	2.22%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1225574338	T -> DEL	N	N	silent_mutation	Average:36.149; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg1225574338	T -> G	LOC_Os12g41250.1	upstream_gene_variant ; 2117.0bp to feature; MODIFIER	silent_mutation	Average:36.149; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg1225574338	T -> G	LOC_Os12g41240.1	downstream_gene_variant ; 254.0bp to feature; MODIFIER	silent_mutation	Average:36.149; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg1225574338	T -> G	LOC_Os12g41240-LOC_Os12g41250	intergenic_region ; MODIFIER	silent_mutation	Average:36.149; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1225574338	NA	2.36E-07	mr1133	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
vg1225574338	3.65E-06	3.65E-06	mr1355	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