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Detailed information for vg1005835090:

Variant ID: vg1005835090 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5835090
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ATATACCATTGAACAGACCAAGGGAGAGCTTGCTGAAGAAGCATGATAGCAGCAAAACCTGACAAACTATTCTTTGATCAACCCTAATTAACTTTCTGTC[C/T]
CGAGTTTATGTTTGATAGCATATCACTGTCAATGCATTTTGCGACCATCGAACAAGTCTACAGTAAAACGGTTTTGCTATATAAGAGTACATAGGAGTGG

Reverse complement sequence

CCACTCCTATGTACTCTTATATAGCAAAACCGTTTTACTGTAGACTTGTTCGATGGTCGCAAAATGCATTGACAGTGATATGCTATCAAACATAAACTCG[G/A]
GACAGAAAGTTAATTAGGGTTGATCAAAGAATAGTTTGTCAGGTTTTGCTGCTATCATGCTTCTTCAGCAAGCTCTCCCTTGGTCTGTTCAATGGTATAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.00%	2.00%	0.02%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	94.30%	5.70%	0.00%	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	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	89.30%	10.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1005835090	C -> T	LOC_Os10g10560.1	upstream_gene_variant ; 828.0bp to feature; MODIFIER	silent_mutation	Average:51.626; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1005835090	C -> T	LOC_Os10g10570.1	upstream_gene_variant ; 2684.0bp to feature; MODIFIER	silent_mutation	Average:51.626; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1005835090	C -> T	LOC_Os10g10550.1	downstream_gene_variant ; 2878.0bp to feature; MODIFIER	silent_mutation	Average:51.626; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1005835090	C -> T	LOC_Os10g10560-LOC_Os10g10570	intergenic_region ; MODIFIER	silent_mutation	Average:51.626; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005835090	3.17E-06	2.16E-09	mr1062	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