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Detailed information for vg0922304115:

Variant ID: vg0922304115 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22304115
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 42. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTTAACTGCAACCTATATACTTGATCTTTTTCGAATATGTAACAGCTTTACATGTCAATATATTATAAGTAGAGTTAAATTTTCAACTTGATTCTTCA[A/C]
CCTACTATACTTCATAAACAAAAGCAGACTATATTGTGCTCATTAATCAATCTTTCCTTCACGTTTGCTTTTCCCATTAAACAACTGTTCCCCAAGAATT

Reverse complement sequence

AATTCTTGGGGAACAGTTGTTTAATGGGAAAAGCAAACGTGAAGGAAAGATTGATTAATGAGCACAATATAGTCTGCTTTTGTTTATGAAGTATAGTAGG[T/G]
TGAAGAATCAAGTTGAAAATTTAACTCTACTTATAATATATTGACATGTAAAGCTGTTACATATTCGAAAAAGATCAAGTATATAGGTTGCAGTTAAAAG

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	79.80%	1.00%	7.00%	12.17%	NA
All Indica	2759	66.70%	1.60%	11.27%	20.44%	NA
All Japonica	1512	99.70%	0.00%	0.07%	0.20%	NA
Aus	269	92.60%	0.40%	5.95%	1.12%	NA
Indica I	595	46.10%	1.30%	23.19%	29.41%	NA
Indica II	465	56.30%	1.10%	10.75%	31.83%	NA
Indica III	913	83.10%	2.30%	4.38%	10.19%	NA
Indica Intermediate	786	69.20%	1.40%	10.56%	18.83%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	92.20%	1.10%	2.22%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0922304115	A -> DEL	N	N	silent_mutation	Average:51.405; most accessible tissue: Zhenshan97 flower, score: 75.194	N	N	N	N
vg0922304115	A -> C	LOC_Os09g38834.1	upstream_gene_variant ; 3387.0bp to feature; MODIFIER	silent_mutation	Average:51.405; most accessible tissue: Zhenshan97 flower, score: 75.194	N	N	N	N
vg0922304115	A -> C	LOC_Os09g38830.1	intron_variant ; MODIFIER	silent_mutation	Average:51.405; most accessible tissue: Zhenshan97 flower, score: 75.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0922304115	4.39E-06	7.99E-07	mr1804	Ind_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