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Detailed information for vg0141225239:

Variant ID: vg0141225239 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41225239
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.14, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GCCATGGGCATCGCTGGAACAGAGGTTCGTACTACTTACCTCCGTTTCAGGTTATAAGATGTTTTGACTTTGGTCAAAGTCAAATTGCTTTAAGTTTGAC[T/C]
AAGTTTGTAGAAAAAAATATTTTCAATTCAAGACAAATTTATTACAAAAATATATTTAATTATTGATTTAATGAAATTAATTTGGTATTATAAATATTAC

Reverse complement sequence

GTAATATTTATAATACCAAATTAATTTCATTAAATCAATAATTAAATATATTTTTGTAATAAATTTGTCTTGAATTGAAAATATTTTTTTCTACAAACTT[A/G]
GTCAAACTTAAAGCAATTTGACTTTGACCAAAGTCAAAACATCTTATAACCTGAAACGGAGGTAAGTAGTACGAACCTCTGTTCCAGCGATGCCCATGGC

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	62.00%	37.90%	0.08%	0.02%	NA
All Indica	2759	91.10%	8.70%	0.11%	0.04%	NA
All Japonica	1512	3.90%	96.00%	0.07%	0.00%	NA
Aus	269	86.60%	13.40%	0.00%	0.00%	NA
Indica I	595	93.90%	6.10%	0.00%	0.00%	NA
Indica II	465	95.10%	4.90%	0.00%	0.00%	NA
Indica III	913	93.00%	6.90%	0.11%	0.00%	NA
Indica Intermediate	786	84.50%	15.10%	0.25%	0.13%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	5.80%	94.00%	0.20%	0.00%	NA
Japonica Intermediate	241	9.10%	90.90%	0.00%	0.00%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	50.00%	50.00%	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
vg0141225239	T -> DEL	N	N	silent_mutation	Average:47.683; most accessible tissue: Zhenshan97 flag leaf, score: 69.582	N	N	N	N
vg0141225239	T -> C	LOC_Os01g71250.1	downstream_gene_variant ; 1462.0bp to feature; MODIFIER	silent_mutation	Average:47.683; most accessible tissue: Zhenshan97 flag leaf, score: 69.582	N	N	N	N
vg0141225239	T -> C	LOC_Os01g71240.1	intron_variant ; MODIFIER	silent_mutation	Average:47.683; most accessible tissue: Zhenshan97 flag leaf, score: 69.582	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141225239	NA	1.19E-07	mr1659	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
vg0141225239	3.66E-06	3.66E-06	mr1756	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
vg0141225239	NA	1.82E-08	mr1660_2	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