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Detailed information for vg1224010698:

Variant ID: vg1224010698 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24010698
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.09, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

TAAAACGAAATAAAAGCCGTGTAATAGATGGCAAAAAATCGATGGATCCTATCCGACTCAAGCGTCCATCAATTAAGCGTTTTTTTCTGACAGTTTTTTC[T/C]
AGAGCGATTTATTTTTTAATAGACGGTGTTTTTTCTTGCGCGGTTTTTTCAAATCATTTTTTAGAAATGGCGCATTTTTTCTTACATTTTTTTTCCTTGC

Reverse complement sequence

GCAAGGAAAAAAAATGTAAGAAAAAATGCGCCATTTCTAAAAAATGATTTGAAAAAACCGCGCAAGAAAAAACACCGTCTATTAAAAAATAAATCGCTCT[A/G]
GAAAAAACTGTCAGAAAAAAACGCTTAATTGATGGACGCTTGAGTCGGATAGGATCCATCGATTTTTTGCCATCTATTACACGGCTTTTATTTCGTTTTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.90%	4.10%	0.02%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	90.60%	9.30%	0.07%	0.00%	NA
Aus	269	98.50%	1.50%	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	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	90.90%	9.10%	0.00%	0.00%	NA
Tropical Japonica	504	93.30%	6.70%	0.00%	0.00%	NA
Japonica Intermediate	241	84.20%	15.40%	0.41%	0.00%	NA
VI/Aromatic	96	55.20%	44.80%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1224010698	T -> C	LOC_Os12g39040.1	upstream_gene_variant ; 2686.0bp to feature; MODIFIER	silent_mutation	Average:16.939; most accessible tissue: Callus, score: 34.039	N	N	N	N
vg1224010698	T -> C	LOC_Os12g39030.1	downstream_gene_variant ; 689.0bp to feature; MODIFIER	silent_mutation	Average:16.939; most accessible tissue: Callus, score: 34.039	N	N	N	N
vg1224010698	T -> C	LOC_Os12g39030-LOC_Os12g39040	intergenic_region ; MODIFIER	silent_mutation	Average:16.939; most accessible tissue: Callus, score: 34.039	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224010698	1.62E-06	1.62E-06	mr1861	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