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Detailed information for vg0221679698:

Variant ID: vg0221679698 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21679698
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGAAATTGTTTCTCTAATTGAGCCCAAGTATGAATAGAATTTGCCGGTAAAGAAGTAAACCATGTAAAAGCATTACTGGATAAAGATAAAGAAAATAA[G/A]
CGCAATTTAAAAGTATCACTATTAGCCTCACCACATTGCGCTAAAAATTGACCTACATGCTCCCATGTGGTCTTACCATCCTCACCACTAAACTTGGTAA

Reverse complement sequence

TTACCAAGTTTAGTGGTGAGGATGGTAAGACCACATGGGAGCATGTAGGTCAATTTTTAGCGCAATGTGGTGAGGCTAATAGTGATACTTTTAAATTGCG[C/T]
TTATTTTCTTTATCTTTATCCAGTAATGCTTTTACATGGTTTACTTCTTTACCGGCAAATTCTATTCATACTTGGGCTCAATTAGAGAAACAATTTCATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.10%	0.40%	18.07%	15.45%	NA
All Indica	2759	53.00%	0.50%	23.60%	22.83%	NA
All Japonica	1512	95.50%	0.00%	0.40%	4.10%	NA
Aus	269	21.90%	0.70%	68.40%	8.92%	NA
Indica I	595	31.30%	0.50%	14.79%	53.45%	NA
Indica II	465	73.30%	1.10%	16.13%	9.46%	NA
Indica III	913	53.90%	0.30%	34.17%	11.61%	NA
Indica Intermediate	786	56.50%	0.50%	22.39%	20.61%	NA
Temperate Japonica	767	99.30%	0.00%	0.26%	0.39%	NA
Tropical Japonica	504	88.90%	0.00%	0.79%	10.32%	NA
Japonica Intermediate	241	97.10%	0.00%	0.00%	2.90%	NA
VI/Aromatic	96	93.80%	0.00%	6.25%	0.00%	NA
Intermediate	90	76.70%	0.00%	7.78%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0221679698	G -> A	LOC_Os02g36060.1	synonymous_variant ; p.Arg195Arg; LOW	synonymous_codon	Average:11.563; most accessible tissue: Minghui63 flag leaf, score: 18.084	N	N	N	N
vg0221679698	G -> DEL	LOC_Os02g36060.1	N	frameshift_variant	Average:11.563; most accessible tissue: Minghui63 flag leaf, score: 18.084	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221679698	NA	3.71E-06	mr1544	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
vg0221679698	NA	7.61E-06	mr1904	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