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Detailed information for vg0909297791:

Variant ID: vg0909297791 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9297791
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.84, C: 0.17, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTATTCAAAAACTTTTGTGAAATATGTAAAATTATATGCCTACATAAAAATATATTTAACAATGAATCAAATGATATGAAAAGAATTAATAATTACTT[C/A]
AATTTTTTTTAATAAGACGAACGGTCAAATATTTTGAAACGGAGGGAGCATAAAAATGTTCGACTGAGCCGACAAGGATGCACGCTTTCTCATTGCGATT

Reverse complement sequence

AATCGCAATGAGAAAGCGTGCATCCTTGTCGGCTCAGTCGAACATTTTTATGCTCCCTCCGTTTCAAAATATTTGACCGTTCGTCTTATTAAAAAAAATT[G/T]
AAGTAATTATTAATTCTTTTCATATCATTTGATTCATTGTTAAATATATTTTTATGTAGGCATATAATTTTACATATTTCACAAAAGTTTTTGAATAAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.80%	34.30%	2.45%	0.47%	NA
All Indica	2759	86.00%	12.70%	1.34%	0.00%	NA
All Japonica	1512	22.00%	71.70%	4.89%	1.46%	NA
Aus	269	48.30%	50.90%	0.74%	0.00%	NA
Indica I	595	87.70%	9.60%	2.69%	0.00%	NA
Indica II	465	96.80%	1.70%	1.51%	0.00%	NA
Indica III	913	79.60%	19.80%	0.55%	0.00%	NA
Indica Intermediate	786	85.60%	13.20%	1.15%	0.00%	NA
Temperate Japonica	767	12.30%	76.50%	8.34%	2.87%	NA
Tropical Japonica	504	27.80%	71.00%	1.19%	0.00%	NA
Japonica Intermediate	241	40.70%	57.70%	1.66%	0.00%	NA
VI/Aromatic	96	85.40%	14.60%	0.00%	0.00%	NA
Intermediate	90	56.70%	40.00%	3.33%	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
vg0909297791	C -> DEL	N	N	silent_mutation	Average:46.459; most accessible tissue: Callus, score: 84.408	N	N	N	N
vg0909297791	C -> A	LOC_Os09g15260-LOC_Os09g15270	intergenic_region ; MODIFIER	silent_mutation	Average:46.459; most accessible tissue: Callus, score: 84.408	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909297791	NA	3.35E-23	mr1548	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
vg0909297791	NA	3.57E-06	mr1298_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
vg0909297791	NA	8.98E-28	mr1617_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
vg0909297791	NA	2.49E-19	mr1637_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
vg0909297791	1.13E-06	NA	mr1702_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
vg0909297791	NA	1.41E-06	mr1702_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
vg0909297791	NA	7.16E-14	mr1713_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
vg0909297791	NA	4.53E-07	mr1727_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
vg0909297791	NA	3.60E-06	mr1729_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
vg0909297791	NA	7.23E-06	mr1731_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
vg0909297791	NA	1.18E-08	mr1741_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
vg0909297791	NA	6.71E-08	mr1783_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
vg0909297791	NA	2.95E-06	mr1785_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