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Detailed information for vg0100357693:

Variant ID: vg0100357693 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 357693
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, A: 0.04, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

TCTAGATGGATTATTGTATGCATAAGGTAGATTCTTGTGCTATTGTAAGGATTGATTGGCTATTTGCAAATGAAAGAGCTTTTGCTTTTACCTATGCTTC[A/C]
ATGGACCTGCTATTTTTCTGTGGTTCAGCTGGCACATGTGATTGGAGGTTGTAAGCTAGGGAAAATTTTGCAGCTGATGTCCAGAATCTTAACACATCGT

Reverse complement sequence

ACGATGTGTTAAGATTCTGGACATCAGCTGCAAAATTTTCCCTAGCTTACAACCTCCAATCACATGTGCCAGCTGAACCACAGAAAAATAGCAGGTCCAT[T/G]
GAAGCATAGGTAAAAGCAAAAGCTCTTTCATTTGCAAATAGCCAATCAATCCTTACAATAGCACAAGAATCTACCTTATGCATACAATAATCCATCTAGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.00%	49.60%	0.04%	0.36%	NA
All Indica	2759	68.60%	30.80%	0.00%	0.54%	NA
All Japonica	1512	10.60%	89.20%	0.07%	0.07%	NA
Aus	269	88.80%	11.20%	0.00%	0.00%	NA
Indica I	595	98.30%	1.20%	0.00%	0.50%	NA
Indica II	465	65.80%	33.50%	0.00%	0.65%	NA
Indica III	913	48.00%	51.70%	0.00%	0.33%	NA
Indica Intermediate	786	71.90%	27.40%	0.00%	0.76%	NA
Temperate Japonica	767	13.80%	85.90%	0.13%	0.13%	NA
Tropical Japonica	504	8.30%	91.70%	0.00%	0.00%	NA
Japonica Intermediate	241	5.40%	94.60%	0.00%	0.00%	NA
VI/Aromatic	96	30.20%	69.80%	0.00%	0.00%	NA
Intermediate	90	44.40%	53.30%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0100357693	A -> DEL	N	N	silent_mutation	Average:51.95; most accessible tissue: Callus, score: 78.328	N	N	N	N
vg0100357693	A -> C	LOC_Os01g01689.1	intron_variant ; MODIFIER	silent_mutation	Average:51.95; most accessible tissue: Callus, score: 78.328	N	N	N	N
vg0100357693	A -> C	LOC_Os01g01689.3	intron_variant ; MODIFIER	silent_mutation	Average:51.95; most accessible tissue: Callus, score: 78.328	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0100357693	4.46E-07	4.46E-07	mr1529	Jap_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
vg0100357693	NA	3.73E-06	mr1265_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