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Detailed information for vg0413668647:

Variant ID: vg0413668647 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13668647
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.65, T: 0.35, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

ACATGTAGGCCCCACATTTTTTATATAGAATGCTGACTGGACTGCCACGCGTACGCCACGTAGACCAAAACCACCGTGGATTGGGTCGAGGGGGGTAATT[C/T]
GTCCAGTTTGTATAGTTCGGGGTGAAAAATGTCCGGTTTTGTGGTTTAGGGGGGTAATTCAGATGACCGCGATAGTTCGGGGGTTAATTCGTACTTTTTC

Reverse complement sequence

GAAAAAGTACGAATTAACCCCCGAACTATCGCGGTCATCTGAATTACCCCCCTAAACCACAAAACCGGACATTTTTCACCCCGAACTATACAAACTGGAC[G/A]
AATTACCCCCCTCGACCCAATCCACGGTGGTTTTGGTCTACGTGGCGTACGCGTGGCAGTCCAGTCAGCATTCTATATAAAAAATGTGGGGCCTACATGT

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	68.50%	30.90%	0.63%	0.02%	NA
All Indica	2759	96.50%	2.40%	1.05%	0.04%	NA
All Japonica	1512	12.00%	88.00%	0.00%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	98.70%	1.20%	0.17%	0.00%	NA
Indica II	465	95.90%	1.90%	1.94%	0.22%	NA
Indica III	913	96.60%	2.20%	1.20%	0.00%	NA
Indica Intermediate	786	95.20%	3.80%	1.02%	0.00%	NA
Temperate Japonica	767	2.00%	98.00%	0.00%	0.00%	NA
Tropical Japonica	504	18.10%	81.90%	0.00%	0.00%	NA
Japonica Intermediate	241	31.10%	68.90%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	61.10%	37.80%	1.11%	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
vg0413668647	C -> DEL	N	N	silent_mutation	Average:38.299; most accessible tissue: Minghui63 young leaf, score: 51.901	N	N	N	N
vg0413668647	C -> T	LOC_Os04g23910.1	upstream_gene_variant ; 4063.0bp to feature; MODIFIER	silent_mutation	Average:38.299; most accessible tissue: Minghui63 young leaf, score: 51.901	N	N	N	N
vg0413668647	C -> T	LOC_Os04g23890-LOC_Os04g23910	intergenic_region ; MODIFIER	silent_mutation	Average:38.299; most accessible tissue: Minghui63 young leaf, score: 51.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413668647	NA	3.53E-13	mr1010	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
vg0413668647	NA	8.46E-14	mr1592	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
vg0413668647	NA	4.43E-21	mr1010_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
vg0413668647	2.27E-07	1.67E-30	mr1350_2	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
vg0413668647	2.69E-06	9.27E-11	mr1350_2	Jap_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
vg0413668647	NA	1.43E-17	mr1730_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
vg0413668647	1.20E-07	9.84E-09	mr1730_2	Jap_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