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Detailed information for vg0804453676:

Variant ID: vg0804453676 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4453676
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

CATCAGTTGACCATCTAATTTCTATAAAAATAACCATTTTACCCTTTGGATGAACACAAAAAATTATGAATTACATTATTAAAAATGTAAAAGTTTGTCG[C/T]
ATGAGACTATTATAGTTACGAGTTTGTTGTGCAATGCATTATTTATCAAAAAAATATTTTTAGATAATGAAATAAAAAAAATATTTTTTTTAACAAAAGG

Reverse complement sequence

CCTTTTGTTAAAAAAAATATTTTTTTTATTTCATTATCTAAAAATATTTTTTTGATAAATAATGCATTGCACAACAAACTCGTAACTATAATAGTCTCAT[G/A]
CGACAAACTTTTACATTTTTAATAATGTAATTCATAATTTTTTGTGTTCATCCAAAGGGTAAAATGGTTATTTTTATAGAAATTAGATGGTCAACTGATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.80%	8.50%	27.17%	30.51%	NA
All Indica	2759	4.00%	13.90%	44.04%	38.02%	NA
All Japonica	1512	94.80%	0.00%	0.86%	4.30%	NA
Aus	269	1.50%	5.60%	12.27%	80.67%	NA
Indica I	595	6.40%	10.40%	46.89%	36.30%	NA
Indica II	465	5.20%	9.90%	38.71%	46.24%	NA
Indica III	913	1.50%	19.50%	45.78%	33.19%	NA
Indica Intermediate	786	4.50%	12.50%	43.00%	40.08%	NA
Temperate Japonica	767	98.00%	0.00%	0.78%	1.17%	NA
Tropical Japonica	504	88.70%	0.00%	0.60%	10.71%	NA
Japonica Intermediate	241	97.50%	0.00%	1.66%	0.83%	NA
VI/Aromatic	96	14.60%	0.00%	4.17%	81.25%	NA
Intermediate	90	40.00%	2.20%	21.11%	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
vg0804453676	C -> T	LOC_Os08g07900.1	downstream_gene_variant ; 883.0bp to feature; MODIFIER	silent_mutation	Average:12.243; most accessible tissue: Callus, score: 57.265	N	N	N	N
vg0804453676	C -> T	LOC_Os08g07890-LOC_Os08g07900	intergenic_region ; MODIFIER	silent_mutation	Average:12.243; most accessible tissue: Callus, score: 57.265	N	N	N	N
vg0804453676	C -> DEL	N	N	silent_mutation	Average:12.243; most accessible tissue: Callus, score: 57.265	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804453676	1.18E-06	1.18E-06	mr1473	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
vg0804453676	6.41E-06	6.41E-06	mr1473	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
vg0804453676	4.46E-07	4.46E-07	mr1664	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
vg0804453676	2.14E-06	2.14E-06	mr1664	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