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Detailed information for vg0909815072:

Variant ID: vg0909815072 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9815072
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:

AGGTGAAAAAGGTGTAGGTGAGGAAAGAAGCCAAAGCTCCGGAAGTCGTTGCTATCAATGAGGAATATCAAGGTGTTCATGTACCTACTAGAGATGCGGC[A/G]
AAAACTATACAAGCGGAGAAGACTAAAGCCGACGCCGTTGCTGTCGACATCGGCGGTCTGACCGAGCCAGCTGGCCGGTCTAACCGCCAGACAACGGCCG

Reverse complement sequence

CGGCCGTTGTCTGGCGGTTAGACCGGCCAGCTGGCTCGGTCAGACCGCCGATGTCGACAGCAACGGCGTCGGCTTTAGTCTTCTCCGCTTGTATAGTTTT[T/C]
GCCGCATCTCTAGTAGGTACATGAACACCTTGATATTCCTCATTGATAGCAACGACTTCCGGAGCTTTGGCTTCTTTCCTCACCTACACCTTTTTCACCT

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	53.70%	13.60%	17.90%	14.77%	NA
All Indica	2759	42.10%	19.30%	26.75%	11.85%	NA
All Japonica	1512	81.00%	0.50%	1.26%	17.33%	NA
Aus	269	13.00%	35.70%	14.50%	36.80%	NA
Indica I	595	31.10%	3.70%	45.55%	19.66%	NA
Indica II	465	40.60%	14.60%	30.54%	14.19%	NA
Indica III	913	48.70%	35.30%	11.61%	4.38%	NA
Indica Intermediate	786	43.50%	15.40%	27.86%	13.23%	NA
Temperate Japonica	767	81.00%	0.00%	0.26%	18.77%	NA
Tropical Japonica	504	78.00%	1.20%	2.58%	18.25%	NA
Japonica Intermediate	241	87.10%	0.40%	1.66%	10.79%	NA
VI/Aromatic	96	62.50%	2.10%	31.25%	4.17%	NA
Intermediate	90	64.40%	6.70%	22.22%	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
vg0909815072	A -> G	LOC_Os09g16080.1	synonymous_variant ; p.Ala473Ala; LOW	synonymous_codon	Average:34.901; most accessible tissue: Minghui63 root, score: 69.846	N	N	N	N
vg0909815072	A -> DEL	LOC_Os09g16080.1	N	frameshift_variant	Average:34.901; most accessible tissue: Minghui63 root, score: 69.846	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909815072	1.15E-06	1.14E-06	mr1473	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