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Detailed information for vg1223438680:

Variant ID: vg1223438680 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23438680
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, T: 0.08, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TAGATAGTAATTTACCCGTGCTAATGCCACGACAATATTTGTTAACAAAGACCCCCCCCAAAAAAAATACACATAGCTAGAAAATAGATAAATTTATAAA[G/T]
CTAGGTGTGTAATATAACATCACATATACCTTCTTTTACTATGCAATTTGCATACAAATACTTTCGGCCAATCTCAATTTTTTCCCCTTCAGAATGAAAC

Reverse complement sequence

GTTTCATTCTGAAGGGGAAAAAATTGAGATTGGCCGAAAGTATTTGTATGCAAATTGCATAGTAAAAGAAGGTATATGTGATGTTATATTACACACCTAG[C/A]
TTTATAAATTTATCTATTTTCTAGCTATGTGTATTTTTTTTGGGGGGGGTCTTTGTTAACAAATATTGTCGTGGCATTAGCACGGGTAAATTACTATCTA

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	51.40%	42.50%	0.17%	5.92%	NA
All Indica	2759	79.20%	10.60%	0.29%	9.86%	NA
All Japonica	1512	0.60%	98.90%	0.00%	0.46%	NA
Aus	269	71.70%	28.30%	0.00%	0.00%	NA
Indica I	595	86.60%	13.10%	0.34%	0.00%	NA
Indica II	465	55.70%	6.00%	0.22%	38.06%	NA
Indica III	913	89.50%	9.30%	0.11%	1.10%	NA
Indica Intermediate	786	75.70%	13.00%	0.51%	10.81%	NA
Temperate Japonica	767	0.30%	98.80%	0.00%	0.91%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	10.40%	88.50%	0.00%	1.04%	NA
Intermediate	90	35.60%	64.40%	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
vg1223438680	G -> DEL	N	N	silent_mutation	Average:73.259; most accessible tissue: Callus, score: 87.93	N	N	N	N
vg1223438680	G -> T	LOC_Os12g38180.1	upstream_gene_variant ; 3490.0bp to feature; MODIFIER	silent_mutation	Average:73.259; most accessible tissue: Callus, score: 87.93	N	N	N	N
vg1223438680	G -> T	LOC_Os12g38170.1	downstream_gene_variant ; 2086.0bp to feature; MODIFIER	silent_mutation	Average:73.259; most accessible tissue: Callus, score: 87.93	N	N	N	N
vg1223438680	G -> T	LOC_Os12g38170-LOC_Os12g38180	intergenic_region ; MODIFIER	silent_mutation	Average:73.259; most accessible tissue: Callus, score: 87.93	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223438680	8.06E-06	NA	mr1038	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
vg1223438680	4.44E-06	NA	mr1141	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
vg1223438680	4.59E-06	NA	mr1141	Ind_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
vg1223438680	2.33E-06	NA	mr1389	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
vg1223438680	6.40E-06	NA	mr1389	Ind_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
vg1223438680	NA	5.71E-06	mr1681	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
vg1223438680	NA	5.36E-07	mr1797	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
vg1223438680	NA	5.36E-07	mr1801	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
vg1223438680	NA	1.44E-08	mr1986	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
vg1223438680	NA	1.97E-07	mr1272_2	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
vg1223438680	NA	6.28E-08	mr1321_2	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
vg1223438680	NA	9.00E-06	mr1321_2	Ind_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
vg1223438680	NA	4.92E-06	mr1324_2	Ind_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
vg1223438680	NA	3.24E-06	mr1336_2	Ind_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
vg1223438680	1.94E-07	1.93E-06	mr1389_2	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
vg1223438680	8.97E-08	1.34E-08	mr1389_2	Ind_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
vg1223438680	NA	1.83E-08	mr1607_2	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
vg1223438680	3.22E-07	3.22E-07	mr1966_2	Ind_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