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Detailed information for vg0906927363:

Variant ID: vg0906927363 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6927363
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: 232. )

Flanking Sequence (100 bp) in Reference Genome:

TGCTTTTAAATTGCTAGGAACACGTATATAAAAGTTTTATTCACAAATTATTTTTTGTTTGTAAATATGCCGTTTCGCTTATGCTTAAAATAAGCCAAAC[G/A]
ATGGCTTCCAATTAATGTCGATGTTCCTCTCTAATTATTTGCCATGCTATCTGTTGCTGGTACAAAGAACGTAACTGGCCGGTTTCATAAAATGATAATG

Reverse complement sequence

CATTATCATTTTATGAAACCGGCCAGTTACGTTCTTTGTACCAGCAACAGATAGCATGGCAAATAATTAGAGAGGAACATCGACATTAATTGGAAGCCAT[C/T]
GTTTGGCTTATTTTAAGCATAAGCGAAACGGCATATTTACAAACAAAAAATAATTTGTGAATAAAACTTTTATATACGTGTTCCTAGCAATTTAAAAGCA

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	85.60%	4.90%	0.42%	9.14%	NA
All Indica	2759	98.50%	0.80%	0.07%	0.65%	NA
All Japonica	1512	64.90%	13.60%	0.99%	20.57%	NA
Aus	269	74.70%	0.00%	0.37%	24.91%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	98.20%	0.40%	0.00%	1.31%	NA
Indica Intermediate	786	97.50%	1.80%	0.00%	0.76%	NA
Temperate Japonica	767	76.40%	5.90%	1.04%	16.69%	NA
Tropical Japonica	504	56.00%	15.10%	0.79%	28.17%	NA
Japonica Intermediate	241	46.90%	34.90%	1.24%	17.01%	NA
VI/Aromatic	96	66.70%	0.00%	1.04%	32.29%	NA
Intermediate	90	88.90%	4.40%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906927363	G -> DEL	N	N	silent_mutation	Average:39.368; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0906927363	G -> A	LOC_Os09g12220.1	upstream_gene_variant ; 1262.0bp to feature; MODIFIER	silent_mutation	Average:39.368; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0906927363	G -> A	LOC_Os09g12210-LOC_Os09g12220	intergenic_region ; MODIFIER	silent_mutation	Average:39.368; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906927363	2.13E-07	2.13E-07	mr1323_2	Jap_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
vg0906927363	NA	2.91E-07	mr1695_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