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Detailed information for vg1213074936:

Variant ID: vg1213074936 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13074936
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.02, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGCGATAAATGAAGCAGCAGGACAGAGAGAGACTAGAGGATTTTCACAATTAAGACAGGATTTTTATTTTTGAAAATATTGCTAAGGCTTGGGATCTA[A/C]
GGCTCGTCCTACGGTCAAGGGGGCTCTGATACCAACTTGTCACGACCGGAATTAACCCAACGGGCGTTCCATACGTGCGTGCATTATTCCTTGTCCCAGG

Reverse complement sequence

CCTGGGACAAGGAATAATGCACGCACGTATGGAACGCCCGTTGGGTTAATTCCGGTCGTGACAAGTTGGTATCAGAGCCCCCTTGACCGTAGGACGAGCC[T/G]
TAGATCCCAAGCCTTAGCAATATTTTCAAAAATAAAAATCCTGTCTTAATTGTGAAAATCCTCTAGTCTCTCTCTGTCCTGCTGCTTCATTTATCGCCAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.40%	0.20%	10.92%	12.51%	NA
All Indica	2759	82.70%	0.10%	6.96%	10.15%	NA
All Japonica	1512	72.60%	0.10%	9.26%	17.99%	NA
Aus	269	38.70%	0.40%	54.65%	6.32%	NA
Indica I	595	71.40%	0.20%	9.24%	19.16%	NA
Indica II	465	81.10%	0.20%	10.11%	8.60%	NA
Indica III	913	90.80%	0.20%	3.72%	5.26%	NA
Indica Intermediate	786	83.00%	0.00%	7.12%	9.92%	NA
Temperate Japonica	767	87.70%	0.10%	3.13%	9.00%	NA
Tropical Japonica	504	59.50%	0.20%	18.06%	22.22%	NA
Japonica Intermediate	241	51.90%	0.00%	10.37%	37.76%	NA
VI/Aromatic	96	58.30%	1.00%	29.17%	11.46%	NA
Intermediate	90	77.80%	0.00%	10.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213074936	A -> C	LOC_Os12g23120.1	intron_variant ; MODIFIER	silent_mutation	Average:12.922; most accessible tissue: Callus, score: 23.353	N	N	N	N
vg1213074936	A -> DEL	N	N	silent_mutation	Average:12.922; most accessible tissue: Callus, score: 23.353	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213074936	1.31E-06	4.84E-07	mr1209	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
vg1213074936	5.83E-08	5.83E-08	mr1605	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