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Detailed information for vg1208658349:

Variant ID: vg1208658349 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8658349
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATAAGAAAGGGAGAGAAGCGTATACATGGAGAAAAAGAAGAAAGGGAAAAATGGAAAAAAGGGAGGGGAAGCGTAGGTACCCATGTACGTAGGTGCGTA[C/T]
CGAAGGTGGAGAGGTGGAACCTCGTAGTATTTAGTTTGTTCTAAGATCAATTTAATCTAATAGTTTATAATATTGGACCCATTTATTTAAGTGAAAATCA

Reverse complement sequence

TGATTTTCACTTAAATAAATGGGTCCAATATTATAAACTATTAGATTAAATTGATCTTAGAACAAACTAAATACTACGAGGTTCCACCTCTCCACCTTCG[G/A]
TACGCACCTACGTACATGGGTACCTACGCTTCCCCTCCCTTTTTTCCATTTTTCCCTTTCTTCTTTTTCTCCATGTATACGCTTCTCTCCCTTTCTTATT

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	72.70%	8.40%	5.46%	13.39%	NA
All Indica	2759	59.20%	14.10%	7.47%	19.25%	NA
All Japonica	1512	96.80%	0.00%	0.20%	3.04%	NA
Aus	269	65.80%	0.40%	17.47%	16.36%	NA
Indica I	595	70.90%	4.40%	4.03%	20.67%	NA
Indica II	465	72.00%	2.20%	4.95%	20.86%	NA
Indica III	913	38.70%	29.50%	11.94%	19.93%	NA
Indica Intermediate	786	66.50%	10.70%	6.36%	16.41%	NA
Temperate Japonica	767	95.40%	0.00%	0.13%	4.43%	NA
Tropical Japonica	504	97.80%	0.00%	0.40%	1.79%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	83.30%	6.20%	1.04%	9.38%	NA
Intermediate	90	92.20%	3.30%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208658349	C -> DEL	N	N	silent_mutation	Average:7.7; most accessible tissue: Callus, score: 16.447	N	N	N	N
vg1208658349	C -> T	LOC_Os12g15190.1	downstream_gene_variant ; 3659.0bp to feature; MODIFIER	silent_mutation	Average:7.7; most accessible tissue: Callus, score: 16.447	N	N	N	N
vg1208658349	C -> T	LOC_Os12g15180-LOC_Os12g15190	intergenic_region ; MODIFIER	silent_mutation	Average:7.7; most accessible tissue: Callus, score: 16.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208658349	7.38E-06	5.42E-07	mr1509	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