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Detailed information for vg1013452368:

Variant ID: vg1013452368 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13452368
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

GGTCAGCGGCCACGTTCAAGATAGTAGTGTGGTTGAATCGTTGTGCAATATATGGGATTTCGGAGATCTGCACACAGAAAGGAAAATAAAACGGTACTCA[G/A]
TGAAAAGTGTGTGCGAGATGGGTTTCTTTGTAGAGAAGAGTTCGATGACCTACTCGGTTACTGGTTGTTTTGTACCTCCCATTTACTCTGAGCATCTCGC

Reverse complement sequence

GCGAGATGCTCAGAGTAAATGGGAGGTACAAAACAACCAGTAACCGAGTAGGTCATCGAACTCTTCTCTACAAAGAAACCCATCTCGCACACACTTTTCA[C/T]
TGAGTACCGTTTTATTTTCCTTTCTGTGTGCAGATCTCCGAAATCCCATATATTGCACAACGATTCAACCACACTACTATCTTGAACGTGGCCGCTGACC

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	21.50%	3.40%	1.06%	74.04%	NA
All Indica	2759	0.90%	0.40%	1.27%	97.46%	NA
All Japonica	1512	58.50%	9.40%	0.66%	31.42%	NA
Aus	269	0.40%	0.00%	0.00%	99.63%	NA
Indica I	595	0.20%	0.20%	0.17%	99.50%	NA
Indica II	465	2.20%	1.30%	0.86%	95.70%	NA
Indica III	913	0.30%	0.00%	2.63%	97.04%	NA
Indica Intermediate	786	1.30%	0.50%	0.76%	97.46%	NA
Temperate Japonica	767	94.10%	0.30%	0.00%	5.61%	NA
Tropical Japonica	504	7.10%	27.00%	1.79%	64.09%	NA
Japonica Intermediate	241	52.70%	1.70%	0.41%	45.23%	NA
VI/Aromatic	96	79.20%	1.00%	0.00%	19.79%	NA
Intermediate	90	33.30%	7.80%	5.56%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1013452368	G -> A	LOC_Os10g25950.1	upstream_gene_variant ; 1418.0bp to feature; MODIFIER	silent_mutation	Average:5.183; most accessible tissue: Callus, score: 12.347	N	N	N	N
vg1013452368	G -> A	LOC_Os10g25960.1	intron_variant ; MODIFIER	silent_mutation	Average:5.183; most accessible tissue: Callus, score: 12.347	N	N	N	N
vg1013452368	G -> DEL	N	N	silent_mutation	Average:5.183; most accessible tissue: Callus, score: 12.347	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013452368	2.17E-07	NA	mr1533	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