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Detailed information for vg0510071302:

Variant ID: vg0510071302 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 10071302
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGAGTCTCATGAAAGAATCAAACATTTATTAACCAATAATGAGTTATCTATTTCAAGGAACAATGTCGGATAAATATGTAAACATAGTATGTGATACA[G/A]
TCATCTCTATGATTGCCTCTAGGGCATATCACCAACACTCAGCAAGTCATGAGAAACGTGAGCATGAAGACTTCGAAGGGAGGCTGGGTTTACTTCGCAA

Reverse complement sequence

TTGCGAAGTAAACCCAGCCTCCCTTCGAAGTCTTCATGCTCACGTTTCTCATGACTTGCTGAGTGTTGGTGATATGCCCTAGAGGCAATCATAGAGATGA[C/T]
TGTATCACATACTATGTTTACATATTTATCCGACATTGTTCCTTGAAATAGATAACTCATTATTGGTTAATAAATGTTTGATTCTTTCATGAGACTCTTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.20%	8.40%	0.02%	0.42%	NA
All Indica	2759	91.80%	7.70%	0.00%	0.51%	NA
All Japonica	1512	99.60%	0.30%	0.00%	0.07%	NA
Aus	269	35.70%	63.90%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.40%	0.00%	0.22%	NA
Indica III	913	80.70%	18.00%	0.00%	1.31%	NA
Indica Intermediate	786	93.90%	6.00%	0.00%	0.13%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	94.80%	0.00%	0.00%	5.21%	NA
Intermediate	90	92.20%	7.80%	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
vg0510071302	G -> DEL	N	N	silent_mutation	Average:27.14; most accessible tissue: Callus, score: 46.412	N	N	N	N
vg0510071302	G -> A	LOC_Os05g17540.1	upstream_gene_variant ; 3700.0bp to feature; MODIFIER	silent_mutation	Average:27.14; most accessible tissue: Callus, score: 46.412	N	N	N	N
vg0510071302	G -> A	LOC_Os05g17530.1	downstream_gene_variant ; 1954.0bp to feature; MODIFIER	silent_mutation	Average:27.14; most accessible tissue: Callus, score: 46.412	N	N	N	N
vg0510071302	G -> A	LOC_Os05g17530-LOC_Os05g17540	intergenic_region ; MODIFIER	silent_mutation	Average:27.14; most accessible tissue: Callus, score: 46.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0510071302	8.26E-07	NA	mr1529_2	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