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Detailed information for vg0526725308:

Variant ID: vg0526725308 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 26725308
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTGGCATCATGGCTCCCCCGATTAGCTAGTTACTCAGCCAGGGGTGTCCTATTCCACCCATGTGGTCGCACTTGTCTTATGTTCGGATGAAATTCCAA[G/C]
GAAATGGTCCTTAAGTGCAAGAGCGGGAAACCGTACACCCGGTACGTTCCCCGGTCCACGATTTTGGAAATTCATTTAGTTCGCAAGCACCGACCCAGGT

Reverse complement sequence

ACCTGGGTCGGTGCTTGCGAACTAAATGAATTTCCAAAATCGTGGACCGGGGAACGTACCGGGTGTACGGTTTCCCGCTCTTGCACTTAAGGACCATTTC[C/G]
TTGGAATTTCATCCGAACATAAGACAAGTGCGACCACATGGGTGGAATAGGACACCCCTGGCTGAGTAACTAGCTAATCGGGGGAGCCATGATGCCAAGA

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	54.20%	45.50%	0.25%	0.00%	NA
All Indica	2759	88.30%	11.40%	0.29%	0.00%	NA
All Japonica	1512	0.90%	99.00%	0.07%	0.00%	NA
Aus	269	18.20%	81.00%	0.74%	0.00%	NA
Indica I	595	97.80%	1.80%	0.34%	0.00%	NA
Indica II	465	63.90%	35.90%	0.22%	0.00%	NA
Indica III	913	96.10%	3.80%	0.11%	0.00%	NA
Indica Intermediate	786	86.60%	12.80%	0.51%	0.00%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.00%	0.20%	0.00%	NA
Japonica Intermediate	241	0.00%	100.00%	0.00%	0.00%	NA
VI/Aromatic	96	29.20%	69.80%	1.04%	0.00%	NA
Intermediate	90	37.80%	62.20%	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
vg0526725308	G -> C	LOC_Os05g46070.1	upstream_gene_variant ; 3419.0bp to feature; MODIFIER	silent_mutation	Average:37.531; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0526725308	G -> C	LOC_Os05g46070-LOC_Os05g46090	intergenic_region ; MODIFIER	silent_mutation	Average:37.531; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0526725308	3.77E-06	NA	mr1156	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