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Detailed information for vg0105866541:

Variant ID: vg0105866541 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5866541
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.52, C: 0.48, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CCGACGGGAAGAGAAAGAGAGATAAGGGAGAGAGAGGGAGGCAGAAAGGTTGGAAAGAGAATGACATGTGGACCCCGCAAGTCAGTGGATCCTATTATAA[T/C]
TTTTGTGTGTGAATGACAAATTGGTCCCACATATATATTTTTAAATCTAATCTTACATCAGTGCCACGTCAACGCCACATGGGACGAAGACCAAGTCAAC

Reverse complement sequence

GTTGACTTGGTCTTCGTCCCATGTGGCGTTGACGTGGCACTGATGTAAGATTAGATTTAAAAATATATATGTGGGACCAATTTGTCATTCACACACAAAA[A/G]
TTATAATAGGATCCACTGACTTGCGGGGTCCACATGTCATTCTCTTTCCAACCTTTCTGCCTCCCTCTCTCTCCCTTATCTCTCTTTCTCTTCCCGTCGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.60%	24.40%	0.02%	0.00%	NA
All Indica	2759	69.00%	31.00%	0.00%	0.00%	NA
All Japonica	1512	99.40%	0.50%	0.07%	0.00%	NA
Aus	269	4.80%	95.20%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	60.40%	39.60%	0.00%	0.00%	NA
Indica III	913	46.10%	53.90%	0.00%	0.00%	NA
Indica Intermediate	786	77.70%	22.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	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
vg0105866541	T -> C	LOC_Os01g10990.1	downstream_gene_variant ; 2747.0bp to feature; MODIFIER	silent_mutation	Average:55.625; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg0105866541	T -> C	LOC_Os01g11000.1	intron_variant ; MODIFIER	silent_mutation	Average:55.625; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105866541	NA	4.46E-06	mr1236	Ind_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
vg0105866541	5.27E-07	NA	mr1498	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
vg0105866541	8.67E-09	3.73E-15	mr1498	Ind_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
vg0105866541	3.14E-06	NA	mr1769	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
vg0105866541	1.61E-06	3.50E-13	mr1769	Ind_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
vg0105866541	6.25E-07	NA	mr1951	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
vg0105866541	2.79E-08	1.07E-12	mr1951	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
vg0105866541	NA	3.54E-10	mr1769_2	Ind_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