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Detailed information for vg0402234072:

Variant ID: vg0402234072 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2234072
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.61, T: 0.39, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTTCAGCTATAAAGCTGTACCCTATTATTGCATGCAGATTTTCTTCTAATTCACATGTACAATAAAAGGGGTACATCAATGACGAAAATAGTACTATT[C/T]
GGTAGCGAGATATAAAAAGCTACTGAATCTTATAAAGTTAATATGGTACGGCGTAGTTAAGCACAAAAATAAACTTGGACTAACTAGCTAGCTATATAGT

Reverse complement sequence

ACTATATAGCTAGCTAGTTAGTCCAAGTTTATTTTTGTGCTTAACTACGCCGTACCATATTAACTTTATAAGATTCAGTAGCTTTTTATATCTCGCTACC[G/A]
AATAGTACTATTTTCGTCATTGATGTACCCCTTTTATTGTACATGTGAATTAGAAGAAAATCTGCATGCAATAATAGGGTACAGCTTTATAGCTGAAAAC

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	80.00%	6.90%	1.23%	11.93%	NA
All Indica	2759	79.60%	11.20%	0.40%	8.77%	NA
All Japonica	1512	79.80%	0.80%	2.98%	16.40%	NA
Aus	269	90.30%	0.00%	0.00%	9.67%	NA
Indica I	595	96.60%	1.80%	0.17%	1.34%	NA
Indica II	465	97.60%	1.30%	0.22%	0.86%	NA
Indica III	913	60.60%	22.00%	0.66%	16.76%	NA
Indica Intermediate	786	78.20%	11.60%	0.38%	9.80%	NA
Temperate Japonica	767	92.80%	1.00%	3.26%	2.87%	NA
Tropical Japonica	504	70.40%	0.60%	1.59%	27.38%	NA
Japonica Intermediate	241	58.10%	0.40%	4.98%	36.51%	NA
VI/Aromatic	96	53.10%	0.00%	2.08%	44.79%	NA
Intermediate	90	90.00%	4.40%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402234072	C -> DEL	N	N	silent_mutation	Average:64.75; most accessible tissue: Zhenshan97 flower, score: 88.571	N	N	N	N
vg0402234072	C -> T	LOC_Os04g04650.1	upstream_gene_variant ; 2496.0bp to feature; MODIFIER	silent_mutation	Average:64.75; most accessible tissue: Zhenshan97 flower, score: 88.571	N	N	N	N
vg0402234072	C -> T	LOC_Os04g04640.1	intron_variant ; MODIFIER	silent_mutation	Average:64.75; most accessible tissue: Zhenshan97 flower, score: 88.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402234072	NA	6.89E-06	mr1117	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
vg0402234072	2.75E-07	1.40E-07	mr1320	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
vg0402234072	NA	1.44E-06	mr1961	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