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Detailed information for vg0900274113:

Variant ID: vg0900274113 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 274113
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

GAGACAGCAAGGCCATGGCAAACTACTTACTTGTGGCTTTAGCAGATTCTGCCCGGTCCTGGCTCCACGGATTACCCCGTGGCACAATTGAATCATGGGC[A/G]
GAACTTCGTGACCACTTCATCGCCAATTTCCAGGGCACCTTCGAACGCCCTGGCACACAGTTTGATCTCTACAACGTTATTCAGAAATCTGGAAAATCCC

Reverse complement sequence

GGGATTTTCCAGATTTCTGAATAACGTTGTAGAGATCAAACTGTGTGCCAGGGCGTTCGAAGGTGCCCTGGAAATTGGCGATGAAGTGGTCACGAAGTTC[T/C]
GCCCATGATTCAATTGTGCCACGGGGTAATCCGTGGAGCCAGGACCGGGCAGAATCTGCTAAAGCCACAAGTAAGTAGTTTGCCATGGCCTTGCTGTCTC

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	50.00%	36.70%	4.08%	9.18%	NA
All Indica	2759	77.10%	10.70%	5.62%	6.56%	NA
All Japonica	1512	1.70%	81.90%	0.79%	15.54%	NA
Aus	269	69.50%	24.50%	3.72%	2.23%	NA
Indica I	595	78.20%	9.90%	5.04%	6.89%	NA
Indica II	465	72.50%	15.50%	8.60%	3.44%	NA
Indica III	913	79.30%	8.10%	4.49%	8.11%	NA
Indica Intermediate	786	76.50%	11.60%	5.60%	6.36%	NA
Temperate Japonica	767	2.90%	66.80%	1.17%	29.20%	NA
Tropical Japonica	504	0.60%	99.20%	0.20%	0.00%	NA
Japonica Intermediate	241	0.40%	94.20%	0.83%	4.56%	NA
VI/Aromatic	96	1.00%	85.40%	7.29%	6.25%	NA
Intermediate	90	25.60%	57.80%	10.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900274113	A -> G	LOC_Os09g01340.1	synonymous_variant ; p.Ala481Ala; LOW	synonymous_codon	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900274113	A -> DEL	LOC_Os09g01340.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900274113	NA	5.88E-08	mr1425	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
vg0900274113	NA	4.48E-06	mr1425_2	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
vg0900274113	5.57E-06	NA	mr1471_2	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