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Detailed information for vg0112054957:

Variant ID: vg0112054957 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12054957
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.82, G: 0.16, A: 0.01, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GAGCAAGAATGAGTACAACCACAGTACTCAGCAAGCCACACCGGGAGATGCATGATTAATACAAGGGGTACAAGGGGATAATAATAGGGGTTATGTTTTG[C/G]
AGTAAACAGTATTCAAAAGTCACTTAATTGCTCAAAGCTATTTTGTAAATACGATCCTAGAGCTACACAATATTATTAATCAAGGCTGTGAACCCTCACG

Reverse complement sequence

CGTGAGGGTTCACAGCCTTGATTAATAATATTGTGTAGCTCTAGGATCGTATTTACAAAATAGCTTTGAGCAATTAAGTGACTTTTGAATACTGTTTACT[G/C]
CAAAACATAACCCCTATTATTATCCCCTTGTACCCCTTGTATTAATCATGCATCTCCCGGTGTGGCTTGCTGAGTACTGTGGTTGTACTCATTCTTGCTC

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	65.80%	33.90%	0.15%	0.23%	NA
All Indica	2759	96.30%	3.00%	0.25%	0.36%	NA
All Japonica	1512	6.00%	94.00%	0.00%	0.00%	NA
Aus	269	87.00%	12.60%	0.00%	0.37%	NA
Indica I	595	97.30%	1.00%	1.18%	0.50%	NA
Indica II	465	96.10%	3.40%	0.00%	0.43%	NA
Indica III	913	97.20%	2.50%	0.00%	0.33%	NA
Indica Intermediate	786	94.80%	5.00%	0.00%	0.25%	NA
Temperate Japonica	767	2.50%	97.50%	0.00%	0.00%	NA
Tropical Japonica	504	12.90%	87.10%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	97.10%	0.00%	0.00%	NA
VI/Aromatic	96	76.00%	24.00%	0.00%	0.00%	NA
Intermediate	90	57.80%	42.20%	0.00%	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
vg0112054957	C -> G	LOC_Os01g21536.1	upstream_gene_variant ; 4971.0bp to feature; MODIFIER	silent_mutation	Average:58.904; most accessible tissue: Zhenshan97 root, score: 70.636	N	N	N	N
vg0112054957	C -> G	LOC_Os01g21542.1	upstream_gene_variant ; 1881.0bp to feature; MODIFIER	silent_mutation	Average:58.904; most accessible tissue: Zhenshan97 root, score: 70.636	N	N	N	N
vg0112054957	C -> G	LOC_Os01g21550.1	upstream_gene_variant ; 2320.0bp to feature; MODIFIER	silent_mutation	Average:58.904; most accessible tissue: Zhenshan97 root, score: 70.636	N	N	N	N
vg0112054957	C -> G	LOC_Os01g21542-LOC_Os01g21550	intergenic_region ; MODIFIER	silent_mutation	Average:58.904; most accessible tissue: Zhenshan97 root, score: 70.636	N	N	N	N
vg0112054957	C -> DEL	N	N	silent_mutation	Average:58.904; most accessible tissue: Zhenshan97 root, score: 70.636	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112054957	NA	4.05E-15	mr1916	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