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Detailed information for vg0510163595:

Variant ID: vg0510163595 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 10163595
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCAGGGGCCCATGAGACCCTATAACATTATGTACCCCTGTAAATGTCCCTTTCATAAGGGTAATCATGTAAATTCCCCTGTACAACCTAGATCCTAGTA[C/G]
TAAGAGCCTGCAACAGGGCTATAAATAGCCCCCTAGGGCCATGTAACGGGGGATCCCAAGTGAAATTAAAAATTTAGTACACTTCATTTTCCCAACCACT

Reverse complement sequence

AGTGGTTGGGAAAATGAAGTGTACTAAATTTTTAATTTCACTTGGGATCCCCCGTTACATGGCCCTAGGGGGCTATTTATAGCCCTGTTGCAGGCTCTTA[G/C]
TACTAGGATCTAGGTTGTACAGGGGAATTTACATGATTACCCTTATGAAAGGGACATTTACAGGGGTACATAATGTTATAGGGTCTCATGGGCCCCTGAT

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	96.80%	2.20%	0.95%	0.00%	NA
All Indica	2759	95.00%	3.70%	1.27%	0.00%	NA
All Japonica	1512	99.60%	0.20%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.60%	7.40%	0.00%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	93.30%	3.20%	3.50%	0.00%	NA
Indica Intermediate	786	96.20%	3.60%	0.25%	0.00%	NA
Temperate Japonica	767	99.50%	0.30%	0.26%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	0.00%	5.21%	0.00%	NA
Intermediate	90	97.80%	0.00%	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
vg0510163595	C -> G	LOC_Os05g17650.1	upstream_gene_variant ; 4084.0bp to feature; MODIFIER	silent_mutation	Average:38.662; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg0510163595	C -> G	LOC_Os05g17650-LOC_Os05g17670	intergenic_region ; MODIFIER	silent_mutation	Average:38.662; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0510163595	3.00E-06	1.43E-06	mr1460	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
vg0510163595	4.74E-07	4.74E-07	mr1460	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