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Detailed information for vg0900513558:

Variant ID: vg0900513558 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 513558
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

AATTCTCCTCCCTGCCTCCCCGATTCTTTCAGTTGTCAAACCTGGAGGACAAACCGCCAGCTTCATGTCTGTTCGGAAGTCAATTCAAGCCTCAAGCTTC[G/A]
TGCAGCAGGAGCAAGAAGTTCAGCCCGGAGTCATCGTTCCGCGAAGATCAAGTGGAGTTTTCCCGGAGATGACCTAAACCCAATCTTTCCCAGAAGAGTA

Reverse complement sequence

TACTCTTCTGGGAAAGATTGGGTTTAGGTCATCTCCGGGAAAACTCCACTTGATCTTCGCGGAACGATGACTCCGGGCTGAACTTCTTGCTCCTGCTGCA[C/T]
GAAGCTTGAGGCTTGAATTGACTTCCGAACAGACATGAAGCTGGCGGTTTGTCCTCCAGGTTTGACAACTGAAAGAATCGGGGAGGCAGGGAGGAGAATT

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	93.00%	1.00%	1.12%	4.87%	NA
All Indica	2759	95.60%	0.80%	0.69%	2.94%	NA
All Japonica	1512	88.00%	1.70%	0.86%	9.52%	NA
Aus	269	92.60%	0.00%	7.43%	0.00%	NA
Indica I	595	95.60%	1.00%	0.84%	2.52%	NA
Indica II	465	93.50%	0.20%	1.29%	4.95%	NA
Indica III	913	97.60%	0.50%	0.11%	1.75%	NA
Indica Intermediate	786	94.40%	1.30%	0.89%	3.44%	NA
Temperate Japonica	767	81.10%	0.10%	0.91%	17.86%	NA
Tropical Japonica	504	95.20%	3.60%	0.99%	0.20%	NA
Japonica Intermediate	241	94.60%	2.50%	0.41%	2.49%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	0.00%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900513558	G -> DEL	N	N	silent_mutation	Average:9.829; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0900513558	G -> A	LOC_Os09g01740.1	upstream_gene_variant ; 4612.0bp to feature; MODIFIER	silent_mutation	Average:9.829; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0900513558	G -> A	LOC_Os09g01730.1	downstream_gene_variant ; 1133.0bp to feature; MODIFIER	silent_mutation	Average:9.829; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0900513558	G -> A	LOC_Os09g01720-LOC_Os09g01730	intergenic_region ; MODIFIER	silent_mutation	Average:9.829; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900513558	3.35E-06	NA	mr1722_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