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Detailed information for vg0922305528:

Variant ID: vg0922305528 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22305528
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

TGGAGCTATCCGGTAAGCGAGGGCACAAGCATAGAGTCGAGTAGGCAATATAGTAATGATGAAGAATATTTGTTGTCATCGAGGTACCCTCGATAGTGGA[T/C]
TTTTATCCCTTTTTTTATTGTGCAAGTTTGGATCAATAGTAAACGGTGCTCTCATGTACAATGTCTAGATGGCCCTTTATGATATCCATGCATTTCATTG

Reverse complement sequence

CAATGAAATGCATGGATATCATAAAGGGCCATCTAGACATTGTACATGAGAGCACCGTTTACTATTGATCCAAACTTGCACAATAAAAAAAGGGATAAAA[A/G]
TCCACTATCGAGGGTACCTCGATGACAACAAATATTCTTCATCATTACTATATTGCCTACTCGACTCTATGCTTGTGCCCTCGCTTACCGGATAGCTCCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.90%	22.60%	0.80%	3.77%	NA
All Indica	2759	57.20%	37.90%	1.16%	3.73%	NA
All Japonica	1512	99.50%	0.30%	0.00%	0.20%	NA
Aus	269	72.10%	2.60%	1.49%	23.79%	NA
Indica I	595	24.00%	74.60%	1.34%	0.00%	NA
Indica II	465	47.70%	44.30%	0.65%	7.31%	NA
Indica III	913	80.70%	13.90%	1.53%	3.83%	NA
Indica Intermediate	786	60.70%	34.10%	0.89%	4.33%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.20%	0.00%	0.60%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	78.90%	10.00%	2.22%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0922305528	T -> DEL	N	N	silent_mutation	Average:45.819; most accessible tissue: Callus, score: 81.307	N	N	N	N
vg0922305528	T -> C	LOC_Os09g38834.1	upstream_gene_variant ; 1974.0bp to feature; MODIFIER	silent_mutation	Average:45.819; most accessible tissue: Callus, score: 81.307	N	N	N	N
vg0922305528	T -> C	LOC_Os09g38830.1	downstream_gene_variant ; 5.0bp to feature; MODIFIER	silent_mutation	Average:45.819; most accessible tissue: Callus, score: 81.307	N	N	N	N
vg0922305528	T -> C	LOC_Os09g38830-LOC_Os09g38834	intergenic_region ; MODIFIER	silent_mutation	Average:45.819; most accessible tissue: Callus, score: 81.307	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0922305528	3.31E-06	NA	mr1600	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
vg0922305528	5.64E-06	NA	mr1600	Ind_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
vg0922305528	NA	3.21E-06	mr1582_2	Ind_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