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Detailed information for vg1129015783:

Variant ID: vg1129015783 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 29015783
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, C: 0.10, A: 0.01, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TAGAAGTTGAATTTGAACTTGCATGTTTGTGGAGTGATATATTACATGTTAATACATATTCTCAAATTTTTTCAATTTTTTCATAACCATTTGAGTGACA[C/T]
GTAAACAATGATAACAATGAGGGATATCCCCTCAAGGGATCAAACGAGGGGGGTATCACATCAGCAAGTTACGTCATTCACTAACCTGCATTTATTTGTC

Reverse complement sequence

GACAAATAAATGCAGGTTAGTGAATGACGTAACTTGCTGATGTGATACCCCCCTCGTTTGATCCCTTGAGGGGATATCCCTCATTGTTATCATTGTTTAC[G/A]
TGTCACTCAAATGGTTATGAAAAAATTGAAAAAATTTGAGAATATGTATTAACATGTAATATATCACTCCACAAACATGCAAGTTCAAATTCAACTTCTA

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	32.10%	21.20%	0.68%	46.00%	NA
All Indica	2759	5.40%	20.00%	0.72%	73.87%	NA
All Japonica	1512	83.90%	10.80%	0.26%	5.03%	NA
Aus	269	12.60%	75.50%	2.97%	8.92%	NA
Indica I	595	3.50%	7.10%	0.67%	88.74%	NA
Indica II	465	7.30%	10.10%	0.43%	82.15%	NA
Indica III	913	3.50%	33.30%	0.33%	62.87%	NA
Indica Intermediate	786	7.90%	20.20%	1.40%	70.48%	NA
Temperate Japonica	767	85.50%	6.90%	0.26%	7.30%	NA
Tropical Japonica	504	82.10%	13.90%	0.40%	3.57%	NA
Japonica Intermediate	241	82.20%	17.00%	0.00%	0.83%	NA
VI/Aromatic	96	29.20%	66.70%	0.00%	4.17%	NA
Intermediate	90	43.30%	21.10%	0.00%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1129015783	C -> T	LOC_Os11g48110.1	downstream_gene_variant ; 1039.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1129015783	C -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1129015783	6.79E-07	5.49E-06	mr1662	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