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Detailed information for vg0429378053:

Variant ID: vg0429378053 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 29378053
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, G: 0.02, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAAATCATACATCACATAAGAGATATTGTTATTCGAAGCTTGGGTTTTTGGATTTTGACTCTCCACAAGTAGTAATACTATAGCATTACTACTCGTTA[C/G]
TAATATGTGTTGTGCGTTACTACAATCCCATCGCGACGTTAATGTAAGTGTGCGCAGTAAAGACCATAAGTTTGTAGTAACAATGTGTCTTATTGCAATT

Reverse complement sequence

AATTGCAATAAGACACATTGTTACTACAAACTTATGGTCTTTACTGCGCACACTTACATTAACGTCGCGATGGGATTGTAGTAACGCACAACACATATTA[G/C]
TAACGAGTAGTAATGCTATAGTATTACTACTTGTGGAGAGTCAAAATCCAAAAACCCAAGCTTCGAATAACAATATCTCTTATGTGATGTATGATTTTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.20%	0.80%	0.04%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	97.50%	2.40%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	95.20%	4.60%	0.26%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0429378053	C -> G	LOC_Os04g49230-LOC_Os04g49240	intergenic_region ; MODIFIER	silent_mutation	Average:39.543; most accessible tissue: Minghui63 root, score: 65.927	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0429378053	1.24E-06	6.89E-06	mr1403_2	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
vg0429378053	NA	7.52E-06	mr1757_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