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Detailed information for vg0816231145:

Variant ID: vg0816231145 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16231145
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCAGCGAGAAACAATTGCTAATAAGCAAAGAAAGACGGTAAATGCAAACCAACCTTTAGTTGGTACACACCAAATTGATACTATATATCAAGCAAATC[A/G]
TGATAGTCTGCAACCTAGCTCGGTGGTGCACAATGCTGAGACTAGGAATTCGGAAGACCATAGACACATTGTTTTGGGAGATCACGATGGGTCTATAAGG

Reverse complement sequence

CCTTATAGACCCATCGTGATCTCCCAAAACAATGTGTCTATGGTCTTCCGAATTCCTAGTCTCAGCATTGTGCACCACCGAGCTAGGTTGCAGACTATCA[T/C]
GATTTGCTTGATATATAGTATCAATTTGGTGTGTACCAACTAAAGGTTGGTTTGCATTTACCGTCTTTCTTTGCTTATTAGCAATTGTTTCTCGCTGAGT

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	40.00%	8.80%	36.18%	15.04%	NA
All Indica	2759	20.30%	14.50%	54.58%	10.69%	NA
All Japonica	1512	74.90%	0.10%	4.96%	19.97%	NA
Aus	269	19.70%	3.00%	42.75%	34.57%	NA
Indica I	595	42.90%	12.60%	37.48%	7.06%	NA
Indica II	465	21.10%	9.90%	55.70%	13.33%	NA
Indica III	913	3.40%	18.30%	66.37%	11.94%	NA
Indica Intermediate	786	22.30%	14.10%	53.18%	10.43%	NA
Temperate Japonica	767	98.60%	0.00%	0.00%	1.43%	NA
Tropical Japonica	504	37.70%	0.40%	13.89%	48.02%	NA
Japonica Intermediate	241	77.60%	0.00%	2.07%	20.33%	NA
VI/Aromatic	96	92.70%	0.00%	1.04%	6.25%	NA
Intermediate	90	63.30%	5.60%	14.44%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816231145	A -> G	LOC_Os08g26690.1	intron_variant ; MODIFIER	silent_mutation	Average:7.959; most accessible tissue: Callus, score: 16.525	N	N	N	N
vg0816231145	A -> DEL	N	N	silent_mutation	Average:7.959; most accessible tissue: Callus, score: 16.525	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816231145	2.16E-06	NA	mr1226_2	Jap_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
vg0816231145	4.90E-06	NA	mr1437_2	Jap_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