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Detailed information for vg1020291609:

Variant ID: vg1020291609 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 20291609
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: 39. )

Flanking Sequence (100 bp) in Reference Genome:

ACTTAAATCAAGTGATTGGGATAGATCGGTCGCCATGCCGAGACAATATAAATCACTTAGATCAAAATATATACTAACAATGAGATTATAGATGTTCATA[G/T]
CATAGCCGATCAGATAGATCTAGCATGTATCGGCTAATACTCCGATACCACTCTATATTAAGATATTAAAGCAAGCAAAATATATCAAACAGAAGCCTAA

Reverse complement sequence

TTAGGCTTCTGTTTGATATATTTTGCTTGCTTTAATATCTTAATATAGAGTGGTATCGGAGTATTAGCCGATACATGCTAGATCTATCTGATCGGCTATG[C/A]
TATGAACATCTATAATCTCATTGTTAGTATATATTTTGATCTAAGTGATTTATATTGTCTCGGCATGGCGACCGATCTATCCCAATCACTTGATTTAAGT

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	87.50%	0.40%	0.30%	11.79%	NA
All Indica	2759	80.20%	0.70%	0.47%	18.70%	NA
All Japonica	1512	98.40%	0.00%	0.00%	1.59%	NA
Aus	269	97.40%	0.00%	0.00%	2.60%	NA
Indica I	595	77.10%	0.20%	0.34%	22.35%	NA
Indica II	465	67.70%	0.20%	0.43%	31.61%	NA
Indica III	913	88.70%	1.20%	0.77%	9.31%	NA
Indica Intermediate	786	79.90%	0.60%	0.25%	19.21%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	96.20%	0.00%	0.00%	3.77%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	96.90%	2.10%	0.00%	1.04%	NA
Intermediate	90	88.90%	0.00%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1020291609	G -> T	LOC_Os10g37899.1	upstream_gene_variant ; 1597.0bp to feature; MODIFIER	silent_mutation	Average:8.902; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg1020291609	G -> T	LOC_Os10g37880-LOC_Os10g37899	intergenic_region ; MODIFIER	silent_mutation	Average:8.902; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg1020291609	G -> DEL	N	N	silent_mutation	Average:8.902; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1020291609	3.95E-06	NA	mr1962	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