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Detailed information for vg0123152758:

Variant ID: vg0123152758 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23152758
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ATTACCTACAAAAGAACTAAGCTGTTGCTAGGCTTGTTAGCTCCAAATCTGAATCTTATACTCCTTCCGTCCAATCTGGCTCGTAAACTTGAACTACAAG[T/G]
TCTGTAGCTTAGCCGCCTCCCAAAAACCTGCAAGAAGTAAGAAGTGGGCTCGCTTGTTTCATTCGATATAAGTAGCTAAAATTTCTTGGTTTTGTCTTTT

Reverse complement sequence

AAAAGACAAAACCAAGAAATTTTAGCTACTTATATCGAATGAAACAAGCGAGCCCACTTCTTACTTCTTGCAGGTTTTTGGGAGGCGGCTAAGCTACAGA[A/C]
CTTGTAGTTCAAGTTTACGAGCCAGATTGGACGGAAGGAGTATAAGATTCAGATTTGGAGCTAACAAGCCTAGCAACAGCTTAGTTCTTTTGTAGGTAAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.90%	7.20%	0.17%	4.74%	NA
All Indica	2759	86.30%	5.50%	0.22%	7.94%	NA
All Japonica	1512	89.00%	10.80%	0.13%	0.13%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	76.60%	14.30%	0.50%	8.57%	NA
Indica II	465	96.10%	0.90%	0.22%	2.80%	NA
Indica III	913	91.50%	1.60%	0.00%	6.90%	NA
Indica Intermediate	786	81.80%	6.20%	0.25%	11.70%	NA
Temperate Japonica	767	99.00%	0.90%	0.13%	0.00%	NA
Tropical Japonica	504	72.00%	27.60%	0.00%	0.40%	NA
Japonica Intermediate	241	92.50%	7.10%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	7.80%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123152758	T -> G	LOC_Os01g40930.1	upstream_gene_variant ; 402.0bp to feature; MODIFIER	silent_mutation	Average:37.442; most accessible tissue: Callus, score: 64.016	N	N	N	N
vg0123152758	T -> G	LOC_Os01g40920-LOC_Os01g40930	intergenic_region ; MODIFIER	silent_mutation	Average:37.442; most accessible tissue: Callus, score: 64.016	N	N	N	N
vg0123152758	T -> DEL	N	N	silent_mutation	Average:37.442; most accessible tissue: Callus, score: 64.016	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123152758	6.52E-06	1.96E-06	mr1134	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0123152758	9.53E-07	1.24E-06	mr1504	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
vg0123152758	NA	1.17E-06	mr1696	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251