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Detailed information for vg0206494550:

Variant ID: vg0206494550 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6494550
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, C: 0.28, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

AAATCAAGTGGCTGGGCTACAATGAGAGGAACAATTGGATATGCTGCTCCAGGTATGCTTCTAACAGCTACAATCCACGGTTTTCTTTCTAATTTATTCA[C/G]
AAACCTTTCCATTGATCCATACTTAAGTAGATCGTTTTGCTATTCAGATGTGTGCAATTTGTTATGAAAAACTCAAATTCTTGCAAATGATAATTATGCA

Reverse complement sequence

TGCATAATTATCATTTGCAAGAATTTGAGTTTTTCATAACAAATTGCACACATCTGAATAGCAAAACGATCTACTTAAGTATGGATCAATGGAAAGGTTT[G/C]
TGAATAAATTAGAAAGAAAACCGTGGATTGTAGCTGTTAGAAGCATACCTGGAGCAGCATATCCAATTGTTCCTCTCATTGTAGCCCAGCCACTTGATTT

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	72.20%	25.20%	2.56%	0.00%	NA
All Indica	2759	70.50%	29.20%	0.36%	0.00%	NA
All Japonica	1512	89.20%	10.60%	0.20%	0.00%	NA
Aus	269	2.60%	72.50%	24.91%	0.00%	NA
Indica I	595	68.40%	31.60%	0.00%	0.00%	NA
Indica II	465	63.90%	36.10%	0.00%	0.00%	NA
Indica III	913	77.70%	22.10%	0.22%	0.00%	NA
Indica Intermediate	786	67.60%	31.40%	1.02%	0.00%	NA
Temperate Japonica	767	93.70%	6.30%	0.00%	0.00%	NA
Tropical Japonica	504	94.20%	5.60%	0.20%	0.00%	NA
Japonica Intermediate	241	63.90%	35.30%	0.83%	0.00%	NA
VI/Aromatic	96	44.80%	15.60%	39.58%	0.00%	NA
Intermediate	90	78.90%	17.80%	3.33%	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
vg0206494550	C -> G	LOC_Os02g12440.1	downstream_gene_variant ; 3973.0bp to feature; MODIFIER	silent_mutation	Average:34.456; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0206494550	C -> G	LOC_Os02g12460.1	downstream_gene_variant ; 2160.0bp to feature; MODIFIER	silent_mutation	Average:34.456; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0206494550	C -> G	LOC_Os02g12450.1	intron_variant ; MODIFIER	silent_mutation	Average:34.456; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206494550	2.40E-08	2.40E-08	mr1714	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
vg0206494550	NA	4.55E-06	mr1496_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