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Detailed information for vg1005470235:

Variant ID: vg1005470235 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5470235
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

GATGGGGCTATTTATAGATCGCATTGTTGGATCTTCTCTCTCTATTTTAAAGTATACACAAAGGGTGTGTTGGGTAGGTGGTGATGGGAAGTTTTCCGTA[G/T]
GCACACAAAACAAAGCTACTAATTAATGTATGATTAATTAAGTATTAGCTTTAAAAGTTTAAAAAATAATTTAATATTATTTTTTAAAAAACTTTCTTAA

Reverse complement sequence

TTAAGAAAGTTTTTTAAAAAATAATATTAAATTATTTTTTAAACTTTTAAAGCTAATACTTAATTAATCATACATTAATTAGTAGCTTTGTTTTGTGTGC[C/A]
TACGGAAAACTTCCCATCACCACCTACCCAACACACCCTTTGTGTATACTTTAAAATAGAGAGAGAAGATCCAACAATGCGATCTATAAATAGCCCCATC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.30%	14.20%	0.11%	0.36%	NA
All Indica	2759	84.60%	14.60%	0.18%	0.58%	NA
All Japonica	1512	85.40%	14.60%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	92.30%	7.60%	0.17%	0.00%	NA
Indica II	465	93.80%	6.20%	0.00%	0.00%	NA
Indica III	913	73.60%	25.00%	0.22%	1.20%	NA
Indica Intermediate	786	86.10%	13.00%	0.25%	0.64%	NA
Temperate Japonica	767	91.80%	8.20%	0.00%	0.00%	NA
Tropical Japonica	504	75.80%	24.20%	0.00%	0.00%	NA
Japonica Intermediate	241	85.50%	14.50%	0.00%	0.00%	NA
VI/Aromatic	96	64.60%	35.40%	0.00%	0.00%	NA
Intermediate	90	85.60%	13.30%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005470235	G -> T	LOC_Os10g10040.1	upstream_gene_variant ; 2996.0bp to feature; MODIFIER	silent_mutation	Average:86.843; most accessible tissue: Callus, score: 94.887	N	N	N	N
vg1005470235	G -> T	LOC_Os10g10050.1	upstream_gene_variant ; 196.0bp to feature; MODIFIER	silent_mutation	Average:86.843; most accessible tissue: Callus, score: 94.887	N	N	N	N
vg1005470235	G -> T	LOC_Os10g10060.1	downstream_gene_variant ; 697.0bp to feature; MODIFIER	silent_mutation	Average:86.843; most accessible tissue: Callus, score: 94.887	N	N	N	N
vg1005470235	G -> T	LOC_Os10g10050-LOC_Os10g10060	intergenic_region ; MODIFIER	silent_mutation	Average:86.843; most accessible tissue: Callus, score: 94.887	N	N	N	N
vg1005470235	G -> DEL	N	N	silent_mutation	Average:86.843; most accessible tissue: Callus, score: 94.887	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005470235	1.58E-06	9.83E-07	mr1527_2	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