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Detailed information for vg0402231774:

Variant ID: vg0402231774 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2231774
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.66, C: 0.35, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

GGGGAGCTTAAGATTCTATAGCAGCTAGTTGGTAGCCAGCTTATGAGAATCTAGAAAAGCTGGGTTTCCCAACTTCTTAGAATCTGGATCAAAAGCTAGG[A/C]
TGTTTGGGGAGCTTCTGATTTTGGCAAAAGCTGCAGCATCAAGGAGCTCCCCCAAACAGGCCCTGAGTTATCGAGCTCCGAAGTTCTAACACGAACTTTA

Reverse complement sequence

TAAAGTTCGTGTTAGAACTTCGGAGCTCGATAACTCAGGGCCTGTTTGGGGGAGCTCCTTGATGCTGCAGCTTTTGCCAAAATCAGAAGCTCCCCAAACA[T/G]
CCTAGCTTTTGATCCAGATTCTAAGAAGTTGGGAAACCCAGCTTTTCTAGATTCTCATAAGCTGGCTACCAACTAGCTGCTATAGAATCTTAAGCTCCCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.00%	7.20%	0.93%	11.83%	NA
All Indica	2759	79.50%	11.30%	0.29%	8.95%	NA
All Japonica	1512	80.00%	1.60%	2.25%	16.14%	NA
Aus	269	90.70%	0.00%	0.74%	8.55%	NA
Indica I	595	96.50%	2.00%	0.17%	1.34%	NA
Indica II	465	97.60%	1.30%	0.22%	0.86%	NA
Indica III	913	60.70%	22.10%	0.33%	16.87%	NA
Indica Intermediate	786	77.70%	11.60%	0.38%	10.31%	NA
Temperate Japonica	767	93.20%	2.60%	1.56%	2.61%	NA
Tropical Japonica	504	70.80%	0.60%	1.79%	26.79%	NA
Japonica Intermediate	241	57.30%	0.40%	5.39%	36.93%	NA
VI/Aromatic	96	57.30%	0.00%	0.00%	42.71%	NA
Intermediate	90	87.80%	7.80%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402231774	A -> C	LOC_Os04g04650.1	upstream_gene_variant ; 4794.0bp to feature; MODIFIER	silent_mutation	Average:37.268; most accessible tissue: Zhenshan97 young leaf, score: 56.533	N	N	N	N
vg0402231774	A -> C	LOC_Os04g04640.1	intron_variant ; MODIFIER	silent_mutation	Average:37.268; most accessible tissue: Zhenshan97 young leaf, score: 56.533	N	N	N	N
vg0402231774	A -> DEL	N	N	silent_mutation	Average:37.268; most accessible tissue: Zhenshan97 young leaf, score: 56.533	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402231774	NA	4.45E-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
vg0402231774	NA	1.47E-07	mr1244	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
vg0402231774	2.70E-06	1.14E-06	mr1761	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