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Detailed information for vg0820512665:

Variant ID: vg0820512665 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 20512665
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

AGGAGATGGAGGAAGCCTCACCTTCCAAGAAGTGCATTGCTCTCCAAGTCGAAGTTGAAGACAAGGGCAAGGGCAAGGTGAATGAAGCCAATGAGGACTT[A/G]
GAGGAAGAGATTGCCCTTCTTGCTAGAAGGTTCAATGATCTCTTGGAAAGGAGAAAGGAGAGAGGTAGGGACTCCAACTCCAATAGGAGAAGAAATAGAA

Reverse complement sequence

TTCTATTTCTTCTCCTATTGGAGTTGGAGTCCCTACCTCTCTCCTTTCTCCTTTCCAAGAGATCATTGAACCTTCTAGCAAGAAGGGCAATCTCTTCCTC[T/C]
AAGTCCTCATTGGCTTCATTCACCTTGCCCTTGCCCTTGTCTTCAACTTCGACTTGGAGAGCAATGCACTTCTTGGAAGGTGAGGCTTCCTCCATCTCCT

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	69.60%	12.40%	18.01%	0.00%	NA
All Indica	2759	50.10%	20.60%	29.32%	0.00%	NA
All Japonica	1512	97.90%	0.50%	1.59%	0.00%	NA
Aus	269	97.00%	0.70%	2.23%	0.00%	NA
Indica I	595	31.30%	25.40%	43.36%	0.00%	NA
Indica II	465	31.60%	30.30%	38.06%	0.00%	NA
Indica III	913	67.70%	15.10%	17.20%	0.00%	NA
Indica Intermediate	786	54.80%	17.60%	27.61%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	94.40%	0.80%	4.76%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	1.00%	2.08%	0.00%	NA
Intermediate	90	81.10%	7.80%	11.11%	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
vg0820512665	A -> G	LOC_Os08g33040.1	synonymous_variant ; p.Leu212Leu; LOW	synonymous_codon	Average:22.164; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0820512665	3.22E-06	5.45E-07	mr1388_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