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Detailed information for vg0800003353:

Variant ID: vg0800003353 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 3353
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TAATGTGTTTGGCACGTCATGGATTGCGGGTAAAGCGTACATCTACTGCAGTATGAATATCCTCAAAACTATTCGAATAGCCATGCTCGCGGTTATCGGG[C/T]
ATCGGGACTCACTATGGCATCTTGGATAGAAACCTAACTTAAAACTTTACTAAATACTGTTGCATTTAAAACATTATAGGCTTTCTTCCTCTATATTATC

Reverse complement sequence

GATAATATAGAGGAAGAAAGCCTATAATGTTTTAAATGCAACAGTATTTAGTAAAGTTTTAAGTTAGGTTTCTATCCAAGATGCCATAGTGAGTCCCGAT[G/A]
CCCGATAACCGCGAGCATGGCTATTCGAATAGTTTTGAGGATATTCATACTGCAGTAGATGTACGCTTTACCCGCAATCCATGACGTGCCAAACACATTA

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	79.30%	12.70%	4.27%	3.72%	NA
All Indica	2759	76.00%	16.80%	6.34%	0.91%	NA
All Japonica	1512	88.60%	0.70%	0.73%	9.92%	NA
Aus	269	58.00%	38.30%	3.72%	0.00%	NA
Indica I	595	91.90%	4.50%	3.03%	0.50%	NA
Indica II	465	37.40%	39.40%	20.43%	2.80%	NA
Indica III	913	89.90%	9.40%	0.55%	0.11%	NA
Indica Intermediate	786	70.50%	21.20%	7.25%	1.02%	NA
Temperate Japonica	767	97.80%	0.50%	0.26%	1.43%	NA
Tropical Japonica	504	73.80%	1.00%	1.79%	23.41%	NA
Japonica Intermediate	241	90.50%	0.80%	0.00%	8.71%	NA
VI/Aromatic	96	97.90%	1.00%	0.00%	1.04%	NA
Intermediate	90	71.10%	22.20%	6.67%	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
vg0800003353	C -> T	LOC_Os08g01008.1	upstream_gene_variant ; 780.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800003353	C -> T	LOC_Os08g01010.1	downstream_gene_variant ; 3210.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800003353	C -> T	LOC_Os08g01008	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800003353	C -> DEL	N	N	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
vg0800003353	NA	2.08E-07	mr1291	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
vg0800003353	NA	7.27E-12	mr1471	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
vg0800003353	NA	7.38E-08	mr1577	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
vg0800003353	NA	3.50E-06	mr1654	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
vg0800003353	NA	2.38E-07	mr1808	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
vg0800003353	NA	1.30E-09	mr1815	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
vg0800003353	NA	4.58E-07	mr1808_2	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