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Detailed information for vg1020949886:

Variant ID: vg1020949886 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 20949886
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.02, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCTTAAAAACCCTATTTGCGAAAGCTGTTTCTTTGCTTGTGGTCTAGTGTCCGTGCCATCTCAGATCTCAAATCCCCGATCTATCATCGAATTCAATC[C/G]
CGAATCCAAATCCTTCCAAATTAATCCCTCCGCAAAAGTCTATTTCGCCTCCCCCGGGTTCGATGGGCCGAATCCCTCTCGGCCCATCTCCCTTCCCGTC

Reverse complement sequence

GACGGGAAGGGAGATGGGCCGAGAGGGATTCGGCCCATCGAACCCGGGGGAGGCGAAATAGACTTTTGCGGAGGGATTAATTTGGAAGGATTTGGATTCG[G/C]
GATTGAATTCGATGATAGATCGGGGATTTGAGATCTGAGATGGCACGGACACTAGACCACAAGCAAAGAAACAGCTTTCGCAAATAGGGTTTTTAAGAGA

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	43.90%	0.30%	0.47%	55.31%	NA
All Indica	2759	12.10%	0.50%	0.47%	86.92%	NA
All Japonica	1512	98.70%	0.00%	0.07%	1.19%	NA
Aus	269	38.30%	0.00%	2.60%	59.11%	NA
Indica I	595	6.90%	1.20%	1.01%	90.92%	NA
Indica II	465	33.30%	0.20%	0.22%	66.24%	NA
Indica III	913	1.40%	0.00%	0.11%	98.47%	NA
Indica Intermediate	786	15.90%	0.80%	0.64%	82.70%	NA
Temperate Japonica	767	98.80%	0.00%	0.00%	1.17%	NA
Tropical Japonica	504	99.20%	0.00%	0.20%	0.60%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	60.00%	0.00%	1.11%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1020949886	C -> G	LOC_Os10g39230.1	upstream_gene_variant ; 1923.0bp to feature; MODIFIER	silent_mutation	Average:58.705; most accessible tissue: Minghui63 young leaf, score: 87.373	N	N	N	N
vg1020949886	C -> G	LOC_Os10g39230-LOC_Os10g39250	intergenic_region ; MODIFIER	silent_mutation	Average:58.705; most accessible tissue: Minghui63 young leaf, score: 87.373	N	N	N	N
vg1020949886	C -> DEL	N	N	silent_mutation	Average:58.705; most accessible tissue: Minghui63 young leaf, score: 87.373	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1020949886	NA	2.82E-06	mr1622	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