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Detailed information for vg0404520455:

Variant ID: vg0404520455 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4520455
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.77, C: 0.23, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTAACTATATATAGCACAAAATGCCTTGTTTACCCTTGCTCATTTGATCCTATTTTATCAAAGCTTTTAGTTAGTTTGAGCTGGTTTTGTATATTGGA[C/A]
ATATCGAGAAAGATTTGTGAAATACTCCCTCCATCTACTTTTAATAGTCATATTCTACTTATCATCTATTTAAATATGCTACTAGTCATTCCTCGTAAAC

Reverse complement sequence

GTTTACGAGGAATGACTAGTAGCATATTTAAATAGATGATAAGTAGAATATGACTATTAAAAGTAGATGGAGGGAGTATTTCACAAATCTTTCTCGATAT[G/T]
TCCAATATACAAAACCAGCTCAAACTAACTAAAAGCTTTGATAAAATAGGATCAAATGAGCAAGGGTAAACAAGGCATTTTGTGCTATATATAGTTAACA

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	58.80%	40.90%	0.30%	0.00%	NA
All Indica	2759	57.60%	42.20%	0.22%	0.00%	NA
All Japonica	1512	64.70%	35.10%	0.13%	0.00%	NA
Aus	269	43.50%	56.10%	0.37%	0.00%	NA
Indica I	595	92.30%	7.70%	0.00%	0.00%	NA
Indica II	465	29.70%	70.10%	0.22%	0.00%	NA
Indica III	913	50.70%	49.20%	0.11%	0.00%	NA
Indica Intermediate	786	55.70%	43.80%	0.51%	0.00%	NA
Temperate Japonica	767	87.40%	12.60%	0.00%	0.00%	NA
Tropical Japonica	504	25.00%	74.60%	0.40%	0.00%	NA
Japonica Intermediate	241	75.90%	24.10%	0.00%	0.00%	NA
VI/Aromatic	96	45.80%	52.10%	2.08%	0.00%	NA
Intermediate	90	57.80%	38.90%	3.33%	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
vg0404520455	C -> A	LOC_Os04g08415.1	downstream_gene_variant ; 304.0bp to feature; MODIFIER	silent_mutation	Average:42.524; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0404520455	C -> A	LOC_Os04g08410-LOC_Os04g08415	intergenic_region ; MODIFIER	silent_mutation	Average:42.524; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404520455	NA	6.17E-08	mr1062_2	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
vg0404520455	NA	6.85E-06	mr1349_2	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
vg0404520455	6.79E-06	4.95E-08	mr1449_2	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
vg0404520455	NA	3.20E-12	mr1715_2	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
vg0404520455	NA	2.64E-06	mr1732_2	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
vg0404520455	NA	2.50E-06	mr1895_2	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