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Detailed information for vg0822915714:

Variant ID: vg0822915714 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 22915714
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTTATTATTGCCGAAATCATGTTTCGACAATTAGTTTGGTGTGGCACTTGTTGGAAATATGATCATAAATCGGTATATTTTAATCCAAAATGTTAAGA[C/A]
AATAATCATGGCATAAACAGTGTAGGGTGATCTAGTAAAAACATGTAACATAACCAGTAGCATACTATCATGCGCATCATAAATATCAGGAACAAGAACA

Reverse complement sequence

TGTTCTTGTTCCTGATATTTATGATGCGCATGATAGTATGCTACTGGTTATGTTACATGTTTTTACTAGATCACCCTACACTGTTTATGCCATGATTATT[G/T]
TCTTAACATTTTGGATTAAAATATACCGATTTATGATCATATTTCCAACAAGTGCCACACCAAACTAATTGTCGAAACATGATTTCGGCAATAATAAAAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.50%	33.90%	11.13%	0.47%	NA
All Indica	2759	23.70%	56.70%	18.81%	0.80%	NA
All Japonica	1512	98.70%	1.00%	0.26%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	2.70%	80.00%	17.31%	0.00%	NA
Indica II	465	25.60%	56.10%	18.06%	0.22%	NA
Indica III	913	32.70%	44.40%	20.70%	2.19%	NA
Indica Intermediate	786	28.00%	53.70%	18.19%	0.13%	NA
Temperate Japonica	767	98.20%	1.40%	0.39%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	74.40%	22.20%	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
vg0822915714	C -> A	LOC_Os08g36350.1	upstream_gene_variant ; 368.0bp to feature; MODIFIER	silent_mutation	Average:31.295; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0822915714	C -> A	LOC_Os08g36360.1	downstream_gene_variant ; 1996.0bp to feature; MODIFIER	silent_mutation	Average:31.295; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0822915714	C -> A	LOC_Os08g36340-LOC_Os08g36350	intergenic_region ; MODIFIER	silent_mutation	Average:31.295; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0822915714	C -> DEL	N	N	silent_mutation	Average:31.295; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0822915714	6.89E-06	6.99E-07	mr1956	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