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Detailed information for vg0209726556:

Variant ID: vg0209726556 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9726556
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGATTGCTCATACTGATTCCGTAATTGAATACGTGTTTTAGTGATCCTCCATTTCCTTTTGGAGAAAATCCCTTGTATACGGTATACCTCTGAAATTTTA[C/A]
CTAATCCCTTCTATGCCCCTAAATTTTGCTTACTTCCTTATATACCCCTAAAATTTGATTTTGATCCCTTGCATACCCCTCCCGTCAGTTGACCGTTTAT

Reverse complement sequence

ATAAACGGTCAACTGACGGGAGGGGTATGCAAGGGATCAAAATCAAATTTTAGGGGTATATAAGGAAGTAAGCAAAATTTAGGGGCATAGAAGGGATTAG[G/T]
TAAAATTTCAGAGGTATACCGTATACAAGGGATTTTCTCCAAAAGGAAATGGAGGATCACTAAAACACGTATTCAATTACGGAATCAGTATGAGCAATCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.40%	8.70%	3.11%	30.83%	NA
All Indica	2759	58.60%	0.30%	2.10%	39.04%	NA
All Japonica	1512	62.50%	20.40%	4.76%	12.30%	NA
Aus	269	21.90%	13.80%	4.83%	59.48%	NA
Indica I	595	63.20%	0.20%	3.36%	33.28%	NA
Indica II	465	52.00%	0.20%	1.94%	45.81%	NA
Indica III	913	57.80%	0.00%	1.31%	40.85%	NA
Indica Intermediate	786	59.80%	0.80%	2.16%	37.28%	NA
Temperate Japonica	767	84.50%	1.80%	3.78%	9.91%	NA
Tropical Japonica	504	32.70%	48.20%	3.17%	15.87%	NA
Japonica Intermediate	241	54.80%	21.60%	11.20%	12.45%	NA
VI/Aromatic	96	37.50%	46.90%	4.17%	11.46%	NA
Intermediate	90	63.30%	11.10%	0.00%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0209726556	C -> A	LOC_Os02g17020.1	upstream_gene_variant ; 3636.0bp to feature; MODIFIER	silent_mutation	Average:27.883; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0209726556	C -> A	LOC_Os02g17010-LOC_Os02g17020	intergenic_region ; MODIFIER	silent_mutation	Average:27.883; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0209726556	C -> DEL	N	N	silent_mutation	Average:27.883; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209726556	1.01E-06	NA	mr1113	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