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Detailed information for vg1204926524:

Variant ID: vg1204926524 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4926524
Reference Allele: C	Alternative Allele: T,A
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.15, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCCTGAGGAAGAGGTTAAGTTCGAGGCTTCGGATTTCCTGTTCCGTGGAGCATTGATCAGTGTACTCGCTGACAATATAGTGGACGTGTATATGCACA[C/T,A]
GCCTTCAGGGAAGGACATGTGGGATGCACTTGAGGCCAAGTTCGGAGTTTCCGACGCCGGCAGTGAGCTGTATGTCATGGAGTAGTTCTATGACTACAAG

Reverse complement sequence

CTTGTAGTCATAGAACTACTCCATGACATACAGCTCACTGCCGGCGTCGGAAACTCCGAACTTGGCCTCAAGTGCATCCCACATGTCCTTCCCTGAAGGC[G/A,T]
TGTGCATATACACGTCCACTATATTGTCAGCGAGTACACTGATCAATGCTCCACGGAACAGGAAATCCGAAGCCTCGAACTTAACCTCTTCCTCAGGAGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.00%	46.80%	0.17%	0.00%	A: 0.02%
All Indica	2759	89.10%	10.70%	0.25%	0.00%	A: 0.04%
All Japonica	1512	1.50%	98.50%	0.00%	0.00%	NA
Aus	269	0.40%	99.60%	0.00%	0.00%	NA
Indica I	595	86.70%	12.80%	0.50%	0.00%	NA
Indica II	465	93.50%	6.20%	0.22%	0.00%	NA
Indica III	913	93.60%	5.90%	0.33%	0.00%	A: 0.11%
Indica Intermediate	786	82.80%	17.20%	0.00%	0.00%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	2.60%	97.40%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	27.80%	71.10%	1.11%	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
vg1204926524	C -> A	LOC_Os12g09400.1	missense_variant ; p.Thr99Lys; MODERATE	nonsynonymous_codon ; T99K	Average:16.176; most accessible tissue: Callus, score: 34.202	benign	0.165	DELETERIOUS	0.00
vg1204926524	C -> T	LOC_Os12g09400.1	missense_variant ; p.Thr99Met; MODERATE	nonsynonymous_codon ; T99M	Average:16.176; most accessible tissue: Callus, score: 34.202	benign	-1.445	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204926524	NA	7.02E-06	mr1006	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
vg1204926524	NA	4.88E-13	mr1013	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
vg1204926524	NA	1.43E-28	mr1037	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
vg1204926524	NA	4.09E-06	mr1052	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
vg1204926524	NA	9.63E-33	mr1129	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
vg1204926524	NA	2.59E-14	mr1270	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
vg1204926524	NA	4.36E-06	mr1317	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
vg1204926524	NA	2.31E-11	mr1720	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
vg1204926524	NA	3.19E-31	mr1745	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
vg1204926524	NA	1.40E-12	mr1914	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
vg1204926524	NA	7.02E-06	mr1006_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
vg1204926524	NA	2.41E-31	mr1037_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
vg1204926524	NA	9.45E-06	mr1219_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
vg1204926524	NA	3.37E-16	mr1457_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