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Detailed information for vg0124687217:

Variant ID: vg0124687217 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24687217
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

CATTGTTCAGTGGTGGTCTGATGTAGCTCATTTCCTAGGTGGAAGTTCAACTTAACAGTCTCCACCAAAAGACTGATATATCAAACAGGCACAACTTTGA[G/C]
AACATTTCTTATGAGCCATGAAATTTGGTGGGGATTGTTAGAATAAATGGGCTAGGCCCGATTTTTCTATTAAATCTCAAAGGCCCATAATAAATGTTAA

Reverse complement sequence

TTAACATTTATTATGGGCCTTTGAGATTTAATAGAAAAATCGGGCCTAGCCCATTTATTCTAACAATCCCCACCAAATTTCATGGCTCATAAGAAATGTT[C/G]
TCAAAGTTGTGCCTGTTTGATATATCAGTCTTTTGGTGGAGACTGTTAAGTTGAACTTCCACCTAGGAAATGAGCTACATCAGACCACCACTGAACAATG

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	89.30%	7.40%	0.53%	2.75%	NA
All Indica	2759	82.60%	12.10%	0.80%	4.49%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	94.80%	3.30%	0.00%	1.86%	NA
Indica I	595	95.60%	3.70%	0.00%	0.67%	NA
Indica II	465	94.40%	3.90%	0.00%	1.72%	NA
Indica III	913	71.00%	18.70%	1.53%	8.76%	NA
Indica Intermediate	786	79.40%	15.50%	1.02%	4.07%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	90.00%	5.60%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0124687217	G -> DEL	N	N	silent_mutation	Average:47.709; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0124687217	G -> C	LOC_Os01g43220.1	upstream_gene_variant ; 4175.0bp to feature; MODIFIER	silent_mutation	Average:47.709; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0124687217	G -> C	LOC_Os01g43210.1	downstream_gene_variant ; 507.0bp to feature; MODIFIER	silent_mutation	Average:47.709; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0124687217	G -> C	LOC_Os01g43210-LOC_Os01g43220	intergenic_region ; MODIFIER	silent_mutation	Average:47.709; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124687217	3.55E-08	2.97E-08	mr1438	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