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Detailed information for vg1209050414:

Variant ID: vg1209050414 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9050414
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.67, C: 0.33, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

CGATGGCCTAAGAGGTTCCGACCGGGAGCAGTAGAGAAGTACGATGGGAGCACTGACCCAGAAGAATTTCTTCAAGTCTACTCCACAGTACTCTATGCTG[T/C]
CGGATCGGACGACAACGCGTTGGCGAATTATTTGCCAACTGCGTTAAAAGGCTCTGCGCGTTCATGGTTGATGCACCTTCCGCCCTACTCGATTTCTTCG

Reverse complement sequence

CGAAGAAATCGAGTAGGGCGGAAGGTGCATCAACCATGAACGCGCAGAGCCTTTTAACGCAGTTGGCAAATAATTCGCCAACGCGTTGTCGTCCGATCCG[A/G]
CAGCATAGAGTACTGTGGAGTAGACTTGAAGAAATTCTTCTGGGTCAGTGCTCCCATCGTACTTCTCTACTGCTCCCGGTCGGAACCTCTTAGGCCATCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.40%	35.70%	0.89%	23.99%	NA
All Indica	2759	53.80%	6.30%	1.34%	38.56%	NA
All Japonica	1512	4.20%	94.30%	0.13%	1.32%	NA
Aus	269	80.70%	4.10%	0.00%	15.24%	NA
Indica I	595	35.30%	10.30%	1.85%	52.61%	NA
Indica II	465	51.40%	7.50%	1.94%	39.14%	NA
Indica III	913	65.30%	2.20%	0.77%	31.76%	NA
Indica Intermediate	786	55.70%	7.50%	1.27%	35.50%	NA
Temperate Japonica	767	5.70%	92.40%	0.26%	1.56%	NA
Tropical Japonica	504	3.40%	95.80%	0.00%	0.79%	NA
Japonica Intermediate	241	1.20%	97.10%	0.00%	1.66%	NA
VI/Aromatic	96	71.90%	22.90%	1.04%	4.17%	NA
Intermediate	90	34.40%	57.80%	2.22%	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
vg1209050414	T -> C	LOC_Os12g15880.1	missense_variant ; p.Val433Ala; MODERATE	nonsynonymous_codon ; V433T	Average:26.025; most accessible tissue: Minghui63 young leaf, score: 61.887	benign	-0.254	TOLERATED	0.11
vg1209050414	T -> C	LOC_Os12g15880.1	missense_variant ; p.Val433Ala; MODERATE	nonsynonymous_codon ; V433A	Average:26.025; most accessible tissue: Minghui63 young leaf, score: 61.887	benign	-0.716	TOLERATED	1.00
vg1209050414	T -> DEL	LOC_Os12g15880.1	N	frameshift_variant	Average:26.025; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209050414	NA	1.24E-08	mr1005	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
vg1209050414	2.78E-06	NA	mr1016	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
vg1209050414	4.72E-07	1.45E-06	mr1018	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
vg1209050414	2.05E-06	NA	mr1132	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
vg1209050414	5.08E-06	NA	mr1142	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
vg1209050414	NA	6.36E-19	mr1529	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
vg1209050414	NA	2.76E-20	mr1838	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
vg1209050414	NA	1.60E-08	mr1866	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
vg1209050414	NA	2.97E-51	mr1935	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
vg1209050414	NA	6.80E-07	mr1020_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
vg1209050414	NA	6.80E-15	mr1133_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
vg1209050414	NA	8.50E-17	mr1146_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
vg1209050414	NA	2.67E-15	mr1162_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
vg1209050414	NA	8.49E-11	mr1349_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
vg1209050414	NA	7.62E-14	mr1529_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
vg1209050414	NA	3.46E-45	mr1546_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