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Detailed information for vg1219203688:

Variant ID: vg1219203688 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19203688
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

AAGATCGTTAGGATAATTTCAGTTATCAACAACTAAATAGAAAAAGCCTAACATACATTTTCTCCACCAGATAACCGGGGAGAGCCCCAAGGAGAAGACC[T/C]
GGTTGTATGGACGCCATTTTGATGAGAGCAATGAGCTGATCAGCCAAATCTCAAGGAGATCCATTGATGTCCTCAAAGAGTACTATCGAGTAAGATACAT

Reverse complement sequence

ATGTATCTTACTCGATAGTACTCTTTGAGGACATCAATGGATCTCCTTGAGATTTGGCTGATCAGCTCATTGCTCTCATCAAAATGGCGTCCATACAACC[A/G]
GGTCTTCTCCTTGGGGCTCTCCCCGGTTATCTGGTGGAGAAAATGTATGTTAGGCTTTTTCTATTTAGTTGTTGATAACTGAAATTATCCTAACGATCTT

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	38.80%	36.00%	1.35%	23.85%	NA
All Indica	2759	53.70%	3.70%	2.28%	40.34%	NA
All Japonica	1512	3.10%	96.60%	0.00%	0.33%	NA
Aus	269	98.90%	0.70%	0.00%	0.37%	NA
Indica I	595	48.60%	3.00%	1.51%	46.89%	NA
Indica II	465	77.00%	2.40%	1.72%	18.92%	NA
Indica III	913	44.90%	2.20%	2.30%	50.60%	NA
Indica Intermediate	786	54.10%	6.60%	3.18%	36.13%	NA
Temperate Japonica	767	1.30%	98.30%	0.00%	0.39%	NA
Tropical Japonica	504	2.20%	97.60%	0.00%	0.20%	NA
Japonica Intermediate	241	10.80%	88.80%	0.00%	0.41%	NA
VI/Aromatic	96	14.60%	84.40%	0.00%	1.04%	NA
Intermediate	90	25.60%	65.60%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219203688	T -> C	LOC_Os12g31880.1	missense_variant ; p.Trp470Arg; MODERATE	nonsynonymous_codon ; W470R	Average:47.645; most accessible tissue: Callus, score: 87.713	benign	-0.338	TOLERATED	0.32
vg1219203688	T -> DEL	LOC_Os12g31880.1	N	frameshift_variant	Average:47.645; most accessible tissue: Callus, score: 87.713	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219203688	NA	2.11E-09	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
vg1219203688	NA	3.09E-71	mr1018	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
vg1219203688	NA	8.99E-13	mr1239	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
vg1219203688	NA	1.64E-29	mr1333	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
vg1219203688	NA	1.40E-33	mr1350	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
vg1219203688	NA	5.49E-23	mr1383	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
vg1219203688	NA	3.95E-11	mr1553	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
vg1219203688	NA	7.13E-36	mr1682	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
vg1219203688	NA	5.18E-21	mr1698	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
vg1219203688	1.60E-07	4.07E-42	mr1719	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
vg1219203688	3.03E-06	4.23E-07	mr1719	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
vg1219203688	NA	4.58E-19	mr1754	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
vg1219203688	NA	3.67E-12	mr1940	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
vg1219203688	NA	1.19E-33	mr1944	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
vg1219203688	NA	9.13E-16	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