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Detailed information for vg1208472022:

Variant ID: vg1208472022 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8472022
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAAGCAAAGCTACAAGCCTATAAAGAAGCAATAACAATACATAAAAAGAAAACACAGGGTTCTTTAGGTTATAACAAACATTAAGAGACTTGAACGGGT[C/T]
AATTCGGAGCTCGTATGACCAAGATATGATCATCCGAAGTTTAATGCTGTTATATGGAGATTTGCGGATTATTATAATTAAGCTTTGCAACTATAAAACA

Reverse complement sequence

TGTTTTATAGTTGCAAAGCTTAATTATAATAATCCGCAAATCTCCATATAACAGCATTAAACTTCGGATGATCATATCTTGGTCATACGAGCTCCGAATT[G/A]
ACCCGTTCAAGTCTCTTAATGTTTGTTATAACCTAAAGAACCCTGTGTTTTCTTTTTATGTATTGTTATTGCTTCTTTATAGGCTTGTAGCTTTGCTTGT

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	76.00%	0.50%	4.00%	19.55%	NA
All Indica	2759	62.50%	0.80%	5.44%	31.32%	NA
All Japonica	1512	97.50%	0.00%	1.19%	1.32%	NA
Aus	269	81.80%	0.00%	6.69%	11.52%	NA
Indica I	595	55.80%	0.00%	2.86%	41.34%	NA
Indica II	465	61.30%	2.20%	6.67%	29.89%	NA
Indica III	913	68.00%	0.40%	7.01%	24.53%	NA
Indica Intermediate	786	61.80%	0.90%	4.83%	32.44%	NA
Temperate Japonica	767	95.70%	0.00%	2.35%	1.96%	NA
Tropical Japonica	504	99.20%	0.00%	0.00%	0.79%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	93.80%	0.00%	3.12%	3.12%	NA
Intermediate	90	92.20%	1.10%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208472022	C -> DEL	N	N	silent_mutation	Average:12.655; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1208472022	C -> T	LOC_Os12g14800.1	downstream_gene_variant ; 1752.0bp to feature; MODIFIER	silent_mutation	Average:12.655; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1208472022	C -> T	LOC_Os12g14800-LOC_Os12g14820	intergenic_region ; MODIFIER	silent_mutation	Average:12.655; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208472022	7.47E-07	2.37E-07	mr1265	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
vg1208472022	NA	7.75E-06	mr1528	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