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Detailed information for vg0118946335:

Variant ID: vg0118946335 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 18946335
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, G: 0.22, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

AATAGGATAGCCAACTACTAACTCCAATTCATCTATAGCTAATCTAATAGCTTAGAATAGTTACATACTACACTATTAATACCTGGTCCCACCTGTCATA[G/C]
ACACACTGCGTCTTGGAGTCCATGCTGCAGCTGGCTACAAATCTGTAGCCCGCTGCCATTCTCTCTCCTCATTTATCTACTTAAAATATGTTTGCAGCTG

Reverse complement sequence

CAGCTGCAAACATATTTTAAGTAGATAAATGAGGAGAGAGAATGGCAGCGGGCTACAGATTTGTAGCCAGCTGCAGCATGGACTCCAAGACGCAGTGTGT[C/G]
TATGACAGGTGGGACCAGGTATTAATAGTGTAGTATGTAACTATTCTAAGCTATTAGATTAGCTATAGATGAATTGGAGTTAGTAGTTGGCTATCCTATT

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	73.30%	24.80%	0.36%	1.54%	NA
All Indica	2759	93.00%	3.80%	0.54%	2.61%	NA
All Japonica	1512	40.50%	59.50%	0.00%	0.00%	NA
Aus	269	74.70%	24.90%	0.00%	0.37%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	85.40%	2.60%	0.86%	11.18%	NA
Indica III	913	92.70%	6.90%	0.22%	0.22%	NA
Indica Intermediate	786	92.70%	3.80%	1.15%	2.29%	NA
Temperate Japonica	767	14.70%	85.30%	0.00%	0.00%	NA
Tropical Japonica	504	67.70%	32.30%	0.00%	0.00%	NA
Japonica Intermediate	241	65.60%	34.40%	0.00%	0.00%	NA
VI/Aromatic	96	30.20%	69.80%	0.00%	0.00%	NA
Intermediate	90	61.10%	36.70%	2.22%	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
vg0118946335	G -> DEL	N	N	silent_mutation	Average:71.279; most accessible tissue: Zhenshan97 flag leaf, score: 85.638	N	N	N	N
vg0118946335	G -> C	LOC_Os01g34350.1	upstream_gene_variant ; 669.0bp to feature; MODIFIER	silent_mutation	Average:71.279; most accessible tissue: Zhenshan97 flag leaf, score: 85.638	N	N	N	N
vg0118946335	G -> C	LOC_Os01g34360.1	downstream_gene_variant ; 1017.0bp to feature; MODIFIER	silent_mutation	Average:71.279; most accessible tissue: Zhenshan97 flag leaf, score: 85.638	N	N	N	N
vg0118946335	G -> C	LOC_Os01g34374.1	downstream_gene_variant ; 2486.0bp to feature; MODIFIER	silent_mutation	Average:71.279; most accessible tissue: Zhenshan97 flag leaf, score: 85.638	N	N	N	N
vg0118946335	G -> C	LOC_Os01g34350-LOC_Os01g34360	intergenic_region ; MODIFIER	silent_mutation	Average:71.279; most accessible tissue: Zhenshan97 flag leaf, score: 85.638	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0118946335	6.47E-06	NA	mr1113_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
vg0118946335	NA	1.08E-06	mr1866_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