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Detailed information for vg0114502200:

Variant ID: vg0114502200 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14502200
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 35. )

Flanking Sequence (100 bp) in Reference Genome:

GAGATAGCACGTTGGTCCCGGTCAGATATATGCCAGGCTTCATCGCAACCATTAAAAGCAAGACATTGTATGAAGAAGGGCGAACATGCAGATTGGTAAA[C/T]
TGATGCGTGGTGGACAAGAACGGTCATGATCCCACGTTGCACCTGCTTCTGGCGGAGTGGAGGTAGGTATGGGCTGTCCCATCAGAAGGATCACTCGGAC

Reverse complement sequence

GTCCGAGTGATCCTTCTGATGGGACAGCCCATACCTACCTCCACTCCGCCAGAAGCAGGTGCAACGTGGGATCATGACCGTTCTTGTCCACCACGCATCA[G/A]
TTTACCAATCTGCATGTTCGCCCTTCTTCATACAATGTCTTGCTTTTAATGGTTGCGATGAAGCCTGGCATATATCTGACCGGGACCAACGTGCTATCTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	28.10%	4.50%	16.57%	50.89%	NA
All Indica	2759	2.40%	0.30%	22.94%	74.37%	NA
All Japonica	1512	80.00%	11.60%	6.81%	1.65%	NA
Aus	269	1.90%	0.40%	8.55%	89.22%	NA
Indica I	595	1.70%	0.00%	7.39%	90.92%	NA
Indica II	465	2.80%	0.40%	10.75%	86.02%	NA
Indica III	913	1.60%	0.20%	41.62%	56.52%	NA
Indica Intermediate	786	3.40%	0.60%	20.23%	75.70%	NA
Temperate Japonica	767	78.40%	11.50%	9.00%	1.17%	NA
Tropical Japonica	504	81.70%	11.50%	4.56%	2.18%	NA
Japonica Intermediate	241	81.30%	12.00%	4.56%	2.07%	NA
VI/Aromatic	96	19.80%	12.50%	6.25%	61.46%	NA
Intermediate	90	31.10%	16.70%	20.00%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114502200	C -> T	LOC_Os01g25590.1	upstream_gene_variant ; 1122.0bp to feature; MODIFIER	silent_mutation	Average:6.317; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0114502200	C -> T	LOC_Os01g25580.1	downstream_gene_variant ; 4898.0bp to feature; MODIFIER	silent_mutation	Average:6.317; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0114502200	C -> T	LOC_Os01g25600.1	downstream_gene_variant ; 4473.0bp to feature; MODIFIER	silent_mutation	Average:6.317; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0114502200	C -> T	LOC_Os01g25590-LOC_Os01g25600	intergenic_region ; MODIFIER	silent_mutation	Average:6.317; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0114502200	C -> DEL	N	N	silent_mutation	Average:6.317; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114502200	5.08E-07	7.12E-13	mr1035_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