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Detailed information for vg0922461985:

Variant ID: vg0922461985 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22461985
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

CCGTATGTAGCAACTGATCGAACGGCTGAGATTAAAAGGGTGACGTGGCTTCACCAGAACTCAGCAAAATCCTAATAACTACACTAAGTGGGAATCACTT[G/A]
TATAGTATTATAGGATACGTACCATAAGGTTTCTATATATATGCGCATGTATGGTTGGGAGGATTGATCGATAAGCTAGCCAGATTTCGAATTGGGTGGA

Reverse complement sequence

TCCACCCAATTCGAAATCTGGCTAGCTTATCGATCAATCCTCCCAACCATACATGCGCATATATATAGAAACCTTATGGTACGTATCCTATAATACTATA[C/T]
AAGTGATTCCCACTTAGTGTAGTTATTAGGATTTTGCTGAGTTCTGGTGAAGCCACGTCACCCTTTTAATCTCAGCCGTTCGATCAGTTGCTACATACGG

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	40.40%	5.60%	1.59%	52.50%	NA
All Indica	2759	20.20%	0.10%	1.27%	78.40%	NA
All Japonica	1512	80.20%	16.70%	2.51%	0.60%	NA
Aus	269	1.10%	0.00%	0.37%	98.51%	NA
Indica I	595	34.10%	0.00%	1.51%	64.37%	NA
Indica II	465	10.80%	0.40%	1.08%	87.74%	NA
Indica III	913	14.60%	0.00%	1.10%	84.34%	NA
Indica Intermediate	786	21.90%	0.10%	1.40%	76.59%	NA
Temperate Japonica	767	72.40%	23.60%	3.91%	0.13%	NA
Tropical Japonica	504	94.20%	4.20%	0.60%	0.99%	NA
Japonica Intermediate	241	75.90%	20.70%	2.07%	1.24%	NA
VI/Aromatic	96	87.50%	1.00%	0.00%	11.46%	NA
Intermediate	90	54.40%	7.80%	1.11%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0922461985	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922461985	G -> A	LOC_Os09g39120.1	upstream_gene_variant ; 4392.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922461985	G -> A	LOC_Os09g39130.1	upstream_gene_variant ; 139.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922461985	G -> A	LOC_Os09g39140.1	downstream_gene_variant ; 3807.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922461985	G -> A	LOC_Os09g39130-LOC_Os09g39140	intergenic_region ; MODIFIER	silent_mutation	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
vg0922461985	NA	2.03E-06	mr1013	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
vg0922461985	3.37E-06	NA	mr1034	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
vg0922461985	NA	2.21E-06	mr1034	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