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Detailed information for vg0110539868:

Variant ID: vg0110539868 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 10539868
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, G: 0.08, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCGGGACCGCCTCAGGGGTCTGCGAAACCAGGGCCTAACGGGGGCGATGGTTTTTGGTGACTACTTCCATTGCCGCATCGCACCCCTCCAGGAGCGGT[C/G]
CCGTGGCGCATGGGAGTACACTGGGCCCAACGATCCCATGCGCACCCATGTGGGTGAGCGCTGGGACTAGGGCGAGGAGGGCGCGAAGATGGTGATCTGG

Reverse complement sequence

CCAGATCACCATCTTCGCGCCCTCCTCGCCCTAGTCCCAGCGCTCACCCACATGGGTGCGCATGGGATCGTTGGGCCCAGTGTACTCCCATGCGCCACGG[G/C]
ACCGCTCCTGGAGGGGTGCGATGCGGCAATGGAAGTAGTCACCAAAAACCATCGCCCCCGTTAGGCCCTGGTTTCGCAGACCCCTGAGGCGGTCCCGCAC

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	33.20%	33.10%	0.72%	32.95%	NA
All Indica	2759	1.50%	49.40%	1.05%	48.06%	NA
All Japonica	1512	96.70%	2.40%	0.07%	0.79%	NA
Aus	269	1.10%	28.30%	1.12%	69.52%	NA
Indica I	595	2.00%	18.30%	1.85%	77.82%	NA
Indica II	465	1.30%	38.30%	1.29%	59.14%	NA
Indica III	913	1.10%	75.10%	0.44%	23.33%	NA
Indica Intermediate	786	1.70%	49.60%	1.02%	47.71%	NA
Temperate Japonica	767	98.20%	0.80%	0.13%	0.91%	NA
Tropical Japonica	504	94.80%	4.60%	0.00%	0.60%	NA
Japonica Intermediate	241	95.90%	3.30%	0.00%	0.83%	NA
VI/Aromatic	96	22.90%	72.90%	0.00%	4.17%	NA
Intermediate	90	47.80%	20.00%	1.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0110539868	C -> G	LOC_Os01g18680.1	upstream_gene_variant ; 196.0bp to feature; MODIFIER	silent_mutation	Average:12.432; most accessible tissue: Callus, score: 29.956	N	N	N	N
vg0110539868	C -> G	LOC_Os01g18690.1	downstream_gene_variant ; 1942.0bp to feature; MODIFIER	silent_mutation	Average:12.432; most accessible tissue: Callus, score: 29.956	N	N	N	N
vg0110539868	C -> G	LOC_Os01g18670-LOC_Os01g18680	intergenic_region ; MODIFIER	silent_mutation	Average:12.432; most accessible tissue: Callus, score: 29.956	N	N	N	N
vg0110539868	C -> DEL	N	N	silent_mutation	Average:12.432; most accessible tissue: Callus, score: 29.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0110539868	NA	7.48E-07	mr1690	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
vg0110539868	NA	7.28E-24	mr1888	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
vg0110539868	NA	1.81E-13	mr1216_2	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
vg0110539868	NA	1.33E-16	mr1416_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
vg0110539868	NA	8.38E-46	mr1519_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