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Detailed information for vg0109549917:

Variant ID: vg0109549917 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 9549917
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGACATTTTGCTTGTACTCTTATTCAAAAGAATTTGGAATTATTATTTATTTTTTTGACTTACTTTATTATCCAAAGTACTTTAAGCACAACTTTTCG[T/C]
TTTTTATATTTACACAAATTTTTGAATAAGACGAGTGATCAAACAGTGCAAGCAAAAATGTCAAAAATCCCTTATATTAGGGGACGGATGGAGTAATTTT

Reverse complement sequence

AAAATTACTCCATCCGTCCCCTAATATAAGGGATTTTTGACATTTTTGCTTGCACTGTTTGATCACTCGTCTTATTCAAAAATTTGTGTAAATATAAAAA[A/G]
CGAAAAGTTGTGCTTAAAGTACTTTGGATAATAAAGTAAGTCAAAAAAATAAATAATAATTCCAAATTCTTTTGAATAAGAGTACAAGCAAAATGTCAAA

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	57.00%	43.00%	0.06%	0.00%	NA
All Indica	2759	89.50%	10.50%	0.07%	0.00%	NA
All Japonica	1512	3.30%	96.70%	0.00%	0.00%	NA
Aus	269	14.10%	85.90%	0.00%	0.00%	NA
Indica I	595	94.80%	5.20%	0.00%	0.00%	NA
Indica II	465	83.90%	16.10%	0.00%	0.00%	NA
Indica III	913	91.00%	8.90%	0.11%	0.00%	NA
Indica Intermediate	786	86.90%	13.00%	0.13%	0.00%	NA
Temperate Japonica	767	1.80%	98.20%	0.00%	0.00%	NA
Tropical Japonica	504	5.40%	94.60%	0.00%	0.00%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	57.80%	41.10%	1.11%	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
vg0109549917	T -> C	LOC_Os01g16800.1	upstream_gene_variant ; 3878.0bp to feature; MODIFIER	silent_mutation	Average:29.54; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0109549917	T -> C	LOC_Os01g16800-LOC_Os01g16810	intergenic_region ; MODIFIER	silent_mutation	Average:29.54; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0109549917	4.94E-06	NA	mr1911	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