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Detailed information for vg0801461338:

Variant ID: vg0801461338 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1461338
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.01, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCGTAAGAATTAGCCATACAAACAACAATAGTACTAGTTGTATGCTTGCAACTCCCTACAGTTCCACGAAGATACCACAAATCAAGAATAAAGGGGTT[C/G]
TTTGGATGCCACTCTGTTTATTCTATCAGCAAATTTGACAATGCCACACTTGTGGAAAATTTTGACTAAAAAATGATCAATTTAGGTGTGGGTGTCGATG

Reverse complement sequence

CATCGACACCCACACCTAAATTGATCATTTTTTAGTCAAAATTTTCCACAAGTGTGGCATTGTCAAATTTGCTGATAGAATAAACAGAGTGGCATCCAAA[G/C]
AACCCCTTTATTCTTGATTTGTGGTATCTTCGTGGAACTGTAGGGAGTTGCAAGCATACAACTAGTACTATTGTTGTTTGTATGGCTAATTCTTACGAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.80%	26.50%	0.51%	26.17%	NA
All Indica	2759	22.80%	43.60%	0.76%	32.84%	NA
All Japonica	1512	97.30%	1.90%	0.07%	0.73%	NA
Aus	269	16.40%	0.70%	0.37%	82.53%	NA
Indica I	595	11.60%	62.00%	1.01%	25.38%	NA
Indica II	465	15.10%	79.60%	0.00%	5.38%	NA
Indica III	913	28.40%	13.60%	0.99%	57.06%	NA
Indica Intermediate	786	29.50%	43.10%	0.76%	26.59%	NA
Temperate Japonica	767	96.60%	2.90%	0.13%	0.39%	NA
Tropical Japonica	504	99.00%	0.60%	0.00%	0.40%	NA
Japonica Intermediate	241	95.90%	1.70%	0.00%	2.49%	NA
VI/Aromatic	96	11.50%	3.10%	1.04%	84.38%	NA
Intermediate	90	61.10%	20.00%	0.00%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0801461338	C -> G	LOC_Os08g03160.1	upstream_gene_variant ; 4989.0bp to feature; MODIFIER	silent_mutation	Average:50.176; most accessible tissue: Zhenshan97 root, score: 76.749	N	N	N	N
vg0801461338	C -> G	LOC_Os08g03160-LOC_Os08g03170	intergenic_region ; MODIFIER	silent_mutation	Average:50.176; most accessible tissue: Zhenshan97 root, score: 76.749	N	N	N	N
vg0801461338	C -> DEL	N	N	silent_mutation	Average:50.176; most accessible tissue: Zhenshan97 root, score: 76.749	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801461338	NA	1.73E-10	mr1352	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
vg0801461338	NA	6.45E-06	mr1352	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
vg0801461338	2.44E-06	3.41E-06	mr1375	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
vg0801461338	NA	5.62E-07	mr1850	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