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Detailed information for vg0524201254:

Variant ID: vg0524201254 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 24201254
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, G: 0.03, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTAGGTGGAAACATCTACACCCCCCGTCCCCCCCAAAAGAAAACCCTCTTCTGGGCCTATGTCCATATTCAAACCCATGGAGTGGGTGTTTTTTGGGA[C/G]
AGAGGGAGTATAAATTAAAAATGCTATATTACAATCACCATTTGATGAGAAAACTATAGTCAAATGGTATGCGTTACTCATCTGTTCGCCTTTATGTTGG

Reverse complement sequence

CCAACATAAAGGCGAACAGATGAGTAACGCATACCATTTGACTATAGTTTTCTCATCAAATGGTGATTGTAATATAGCATTTTTAATTTATACTCCCTCT[G/C]
TCCCAAAAAACACCCACTCCATGGGTTTGAATATGGACATAGGCCCAGAAGAGGGTTTTCTTTTGGGGGGGACGGGGGGTGTAGATGTTTCCACCTAAAA

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	90.20%	9.10%	0.70%	0.00%	NA
All Indica	2759	99.50%	0.40%	0.07%	0.00%	NA
All Japonica	1512	71.80%	26.20%	2.05%	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	98.70%	1.10%	0.22%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.50%	0.13%	0.00%	NA
Temperate Japonica	767	87.10%	9.40%	3.52%	0.00%	NA
Tropical Japonica	504	45.80%	53.60%	0.60%	0.00%	NA
Japonica Intermediate	241	77.20%	22.40%	0.41%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0524201254	C -> G	LOC_Os05g41310.1	downstream_gene_variant ; 711.0bp to feature; MODIFIER	silent_mutation	Average:29.77; most accessible tissue: Callus, score: 66.051	N	N	N	N
vg0524201254	C -> G	LOC_Os05g41310-LOC_Os05g41320	intergenic_region ; MODIFIER	silent_mutation	Average:29.77; most accessible tissue: Callus, score: 66.051	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0524201254	4.60E-06	NA	mr1100	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