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Detailed information for vg1218063743:

Variant ID: vg1218063743 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18063743
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TGGTTGTTTGATGGGCTTTAAAGAAGGCCCATAACGTTAATTAATGCTTATTAAAATTTATTATAATCTATAGTTAGGATAATTCGATCTATCAAATCAA[C/T]
AGTGGGATGTTTCTAATTAACGTGGGAGCTTCTTTAGAGTGCCCAATTAGTATAGGTATAGATAGATAGATATATTTCTGATTGTCAAATAATATAAGAT

Reverse complement sequence

ATCTTATATTATTTGACAATCAGAAATATATCTATCTATCTATACCTATACTAATTGGGCACTCTAAAGAAGCTCCCACGTTAATTAGAAACATCCCACT[G/A]
TTGATTTGATAGATCGAATTATCCTAACTATAGATTATAATAAATTTTAATAAGCATTAATTAACGTTATGGGCCTTCTTTAAAGCCCATCAAACAACCA

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	91.20%	8.80%	0.04%	0.00%	NA
All Indica	2759	87.40%	12.50%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	77.70%	22.30%	0.00%	0.00%	NA
Indica I	595	92.90%	7.10%	0.00%	0.00%	NA
Indica II	465	92.50%	7.50%	0.00%	0.00%	NA
Indica III	913	83.70%	16.10%	0.22%	0.00%	NA
Indica Intermediate	786	84.50%	15.50%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg1218063743	C -> T	LOC_Os12g30130.1	upstream_gene_variant ; 4824.0bp to feature; MODIFIER	silent_mutation	Average:48.593; most accessible tissue: Callus, score: 85.684	N	N	N	N
vg1218063743	C -> T	LOC_Os12g30120-LOC_Os12g30130	intergenic_region ; MODIFIER	silent_mutation	Average:48.593; most accessible tissue: Callus, score: 85.684	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218063743	2.63E-06	2.63E-06	mr1321	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
vg1218063743	2.96E-06	2.96E-06	mr1340	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