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Detailed information for vg1218612392:

Variant ID: vg1218612392 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18612392
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, G: 0.02, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

GCCACACCATGCGCTGCCAGCCCGGAGCCAACCCCTGTATGCTCTATCGCCGTGACCATGTTCGCTGCTCCTCCTCGTCTCCTGATCTTCCACCTTCGAG[C/G]
ACCCACACCTGCACGCACGACACACGCATGCAGGAGTAGATTATTTTGTGCAGTGAATATATATAAGAGTGAATTAACTATATATTTTAAGAAAGTTGCA

Reverse complement sequence

TGCAACTTTCTTAAAATATATAGTTAATTCACTCTTATATATATTCACTGCACAAAATAATCTACTCCTGCATGCGTGTGTCGTGCGTGCAGGTGTGGGT[G/C]
CTCGAAGGTGGAAGATCAGGAGACGAGGAGGAGCAGCGAACATGGTCACGGCGATAGAGCATACAGGGGTTGGCTCCGGGCTGGCAGCGCATGGTGTGGC

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	71.40%	27.80%	0.72%	0.00%	NA
All Indica	2759	87.50%	11.50%	0.98%	0.00%	NA
All Japonica	1512	41.40%	58.20%	0.40%	0.00%	NA
Aus	269	93.70%	6.30%	0.00%	0.00%	NA
Indica I	595	83.20%	16.30%	0.50%	0.00%	NA
Indica II	465	89.90%	5.80%	4.30%	0.00%	NA
Indica III	913	86.50%	13.50%	0.00%	0.00%	NA
Indica Intermediate	786	90.60%	8.90%	0.51%	0.00%	NA
Temperate Japonica	767	60.60%	38.90%	0.52%	0.00%	NA
Tropical Japonica	504	8.30%	91.30%	0.40%	0.00%	NA
Japonica Intermediate	241	49.40%	50.60%	0.00%	0.00%	NA
VI/Aromatic	96	22.90%	76.00%	1.04%	0.00%	NA
Intermediate	90	67.80%	32.20%	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
vg1218612392	C -> G	LOC_Os12g30980.1	upstream_gene_variant ; 91.0bp to feature; MODIFIER	silent_mutation	Average:68.934; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg1218612392	C -> G	LOC_Os12g30990.1	downstream_gene_variant ; 1591.0bp to feature; MODIFIER	silent_mutation	Average:68.934; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg1218612392	C -> G	LOC_Os12g30980-LOC_Os12g30990	intergenic_region ; MODIFIER	silent_mutation	Average:68.934; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218612392	5.00E-07	5.93E-09	mr1458	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
vg1218612392	5.98E-08	1.27E-09	mr1458_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