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Detailed information for vg0520708958:

Variant ID: vg0520708958 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 20708958
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTATAACGTAAACATCATGCATGGTACATTTTATTAGCACCTAATATACTTGTCCTAATATTCGTTCAAGCCACATATAGGGTGTAGATTGTGGGCACA[C/G]
GTGAACTCACGTGCAAAAAATCCAACTCCTATATATATAAATTATCCTACTAATTAGAATAAGTCTCATCCAATTCTAGTTTATGTGTGTGTATATATAT

Reverse complement sequence

ATATATATACACACACATAAACTAGAATTGGATGAGACTTATTCTAATTAGTAGGATAATTTATATATATAGGAGTTGGATTTTTTGCACGTGAGTTCAC[G/C]
TGTGCCCACAATCTACACCCTATATGTGGCTTGAACGAATATTAGGACAAGTATATTAGGTGCTAATAAAATGTACCATGCATGATGTTTACGTTATACT

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	93.50%	6.00%	0.53%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	84.30%	14.20%	1.52%	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	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	72.90%	24.30%	2.87%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	87.60%	12.00%	0.41%	0.00%	NA
VI/Aromatic	96	38.50%	61.50%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	2.22%	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
vg0520708958	C -> G	LOC_Os05g34870.1	upstream_gene_variant ; 863.0bp to feature; MODIFIER	silent_mutation	Average:41.944; most accessible tissue: Callus, score: 72.302	N	N	N	N
vg0520708958	C -> G	LOC_Os05g34854-LOC_Os05g34870	intergenic_region ; MODIFIER	silent_mutation	Average:41.944; most accessible tissue: Callus, score: 72.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0520708958	3.15E-06	NA	mr1324	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
vg0520708958	NA	3.62E-06	mr1324	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