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Detailed information for vg0618963218:

Variant ID: vg0618963218 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18963218
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, G: 0.08, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

AGGAGTTGCCCGGGTTTAGGAAGATGAGAAGCCACTATTGCCAATGTGAGGGCCTGATCCAGTTGTCCTGGCTTTCTTGCCTGTGTTTTTGTTGTCATAC[C/G]
TGGTTCTCTGTTATCGAAAGAGGAGTATGGATTGTGTCAGACAAGGAGTAGACGGTGCTGGAGCAAGAGTGGATGGCATCGCTTGGAGCCGGCTTTAATT

Reverse complement sequence

AATTAAAGCCGGCTCCAAGCGATGCCATCCACTCTTGCTCCAGCACCGTCTACTCCTTGTCTGACACAATCCATACTCCTCTTTCGATAACAGAGAACCA[G/C]
GTATGACAACAAAAACACAGGCAAGAAAGCCAGGACAACTGGATCAGGCCCTCACATTGGCAATAGTGGCTTCTCATCTTCCTAAACCCGGGCAACTCCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.30%	25.60%	0.34%	6.73%	NA
All Indica	2759	96.60%	2.60%	0.25%	0.51%	NA
All Japonica	1512	6.80%	73.20%	0.40%	19.58%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.10%	0.80%	0.17%	1.85%	NA
Indica II	465	95.70%	4.10%	0.22%	0.00%	NA
Indica III	913	98.50%	1.30%	0.22%	0.00%	NA
Indica Intermediate	786	94.50%	4.70%	0.38%	0.38%	NA
Temperate Japonica	767	3.80%	65.70%	0.52%	29.99%	NA
Tropical Japonica	504	12.10%	84.30%	0.40%	3.17%	NA
Japonica Intermediate	241	5.40%	73.90%	0.00%	20.75%	NA
VI/Aromatic	96	94.80%	1.00%	0.00%	4.17%	NA
Intermediate	90	60.00%	32.20%	3.33%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618963218	C -> G	LOC_Os06g32610.1	upstream_gene_variant ; 4197.0bp to feature; MODIFIER	silent_mutation	Average:20.407; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg0618963218	C -> G	LOC_Os06g32610-LOC_Os06g32630	intergenic_region ; MODIFIER	silent_mutation	Average:20.407; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg0618963218	C -> DEL	N	N	silent_mutation	Average:20.407; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618963218	NA	1.14E-07	mr1354	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
vg0618963218	5.09E-07	NA	mr1039_2	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
vg0618963218	NA	3.60E-06	mr1062_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
vg0618963218	NA	5.85E-09	mr1354_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
vg0618963218	NA	8.26E-06	mr1354_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