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Detailed information for vg1216968197:

Variant ID: vg1216968197 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16968197
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.06, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

GATCTGTTCATCATTCAAAAACACGATACGCTGCATTTTCACAAATACTTACATTTGACAATTGTTCATTACCCAGATTAATCATCATATGATTCTACAC[A/G]
TCTTGCATTACACGTACACATGGTTAGAGTAGATGTGATCCATTTGTTAGTGGTGACATAAAAATAAAAAAGTTTTCTTCCTCATATTGTTAAACAGAGT

Reverse complement sequence

ACTCTGTTTAACAATATGAGGAAGAAAACTTTTTTATTTTTATGTCACCACTAACAAATGGATCACATCTACTCTAACCATGTGTACGTGTAATGCAAGA[T/C]
GTGTAGAATCATATGATGATTAATCTGGGTAATGAACAATTGTCAAATGTAAGTATTTGTGAAAATGCAGCGTATCGTGTTTTTGAATGATGAACAGATC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.10%	32.10%	0.25%	20.57%	NA
All Indica	2759	19.30%	53.60%	0.36%	26.75%	NA
All Japonica	1512	93.00%	0.70%	0.07%	6.28%	NA
Aus	269	70.30%	0.70%	0.37%	28.62%	NA
Indica I	595	13.40%	82.50%	0.34%	3.70%	NA
Indica II	465	20.90%	17.60%	0.65%	60.86%	NA
Indica III	913	19.80%	59.40%	0.11%	20.70%	NA
Indica Intermediate	786	22.30%	46.20%	0.51%	31.04%	NA
Temperate Japonica	767	96.70%	0.70%	0.00%	2.61%	NA
Tropical Japonica	504	88.10%	0.80%	0.20%	10.91%	NA
Japonica Intermediate	241	91.30%	0.40%	0.00%	8.30%	NA
VI/Aromatic	96	39.60%	6.20%	0.00%	54.17%	NA
Intermediate	90	66.70%	22.20%	0.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216968197	A -> DEL	N	N	silent_mutation	Average:59.035; most accessible tissue: Zhenshan97 panicle, score: 88.062	N	N	N	N
vg1216968197	A -> G	LOC_Os12g28710.1	downstream_gene_variant ; 2549.0bp to feature; MODIFIER	silent_mutation	Average:59.035; most accessible tissue: Zhenshan97 panicle, score: 88.062	N	N	N	N
vg1216968197	A -> G	LOC_Os12g28720.1	intron_variant ; MODIFIER	silent_mutation	Average:59.035; most accessible tissue: Zhenshan97 panicle, score: 88.062	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216968197	NA	1.24E-06	mr1925	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
vg1216968197	1.19E-06	NA	mr1458_2	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
vg1216968197	2.36E-06	NA	mr1458_2	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