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Detailed information for vg1215514024:

Variant ID: vg1215514024 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15514024
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

ATACATTTACCAATTATAAAGGTGTGACTAAATCTTTCATTCCTGCTCAGAATGCGCCAGAAATAGTGGAGGTACCAAATAAAACCACTCAACTTCCACT[C/T]
ACTAAAAAGAGAGGAAGAAGTATGGCCACTCAGCGAGAAACAATTGCTAATAAGCAAAGAAAGACGGTAAATGCAAACCAACCTTTAGTTGGTACACACC

Reverse complement sequence

GGTGTGTACCAACTAAAGGTTGGTTTGCATTTACCGTCTTTCTTTGCTTATTAGCAATTGTTTCTCGCTGAGTGGCCATACTTCTTCCTCTCTTTTTAGT[G/A]
AGTGGAAGTTGAGTGGTTTTATTTGGTACCTCCACTATTTCTGGCGCATTCTGAGCAGGAATGAAAGATTTAGTCACACCTTTATAATTGGTAAATGTAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.10%	3.80%	6.67%	1.48%	NA
All Indica	2759	95.90%	1.20%	2.79%	0.07%	NA
All Japonica	1512	80.60%	3.40%	11.71%	4.30%	NA
Aus	269	63.20%	29.00%	7.81%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	86.00%	2.40%	11.18%	0.43%	NA
Indica III	913	98.00%	1.20%	0.77%	0.00%	NA
Indica Intermediate	786	96.30%	1.40%	2.29%	0.00%	NA
Temperate Japonica	767	97.30%	0.10%	0.52%	2.09%	NA
Tropical Japonica	504	53.00%	8.70%	29.37%	8.93%	NA
Japonica Intermediate	241	85.50%	2.50%	10.37%	1.66%	NA
VI/Aromatic	96	50.00%	13.50%	33.33%	3.12%	NA
Intermediate	90	87.80%	3.30%	8.89%	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
vg1215514024	C -> DEL	N	N	silent_mutation	Average:16.803; most accessible tissue: Zhenshan97 flag leaf, score: 41.874	N	N	N	N
vg1215514024	C -> T	LOC_Os12g26540.1	downstream_gene_variant ; 1862.0bp to feature; MODIFIER	silent_mutation	Average:16.803; most accessible tissue: Zhenshan97 flag leaf, score: 41.874	N	N	N	N
vg1215514024	C -> T	LOC_Os12g26540-LOC_Os12g26560	intergenic_region ; MODIFIER	silent_mutation	Average:16.803; most accessible tissue: Zhenshan97 flag leaf, score: 41.874	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215514024	1.94E-06	1.94E-06	mr1526	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