RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0220796750:

Variant ID: vg0220796750 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20796750
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

CCTAAATGTGTCCAAAATCCCACTCCTATGTGACAATGAGAGCGCCATTAAGATAGCTAATAACCCCGTCCAACATTCCCGAACCAAACACATAGATATT[C/T]
GCCATCATTTCTTGAGAGACCATTCCACAAGAGGCGACATAGATATCCAACATGTGAGAACCGACAAACAATTGGCGGATATGTTCACCAAGCCTCTAGA

Reverse complement sequence

TCTAGAGGCTTGGTGAACATATCCGCCAATTGTTTGTCGGTTCTCACATGTTGGATATCTATGTCGCCTCTTGTGGAATGGTCTCTCAAGAAATGATGGC[G/A]
AATATCTATGTGTTTGGTTCGGGAATGTTGGACGGGGTTATTAGCTATCTTAATGGCGCTCTCATTGTCACATAGGAGTGGGATTTTGGACACATTTAGG

Allele Frequencies:

Search:

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	91.70%	6.30%	1.69%	0.25%	NA
All Indica	2759	91.70%	6.40%	1.59%	0.25%	NA
All Japonica	1512	99.40%	0.50%	0.07%	0.00%	NA
Aus	269	45.40%	40.50%	12.27%	1.86%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	75.50%	19.40%	5.16%	0.00%	NA
Indica III	913	93.60%	5.00%	0.88%	0.44%	NA
Indica Intermediate	786	92.90%	5.20%	1.53%	0.38%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	2.22%	0.00%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0220796750	C -> T	LOC_Os02g34670.1	missense_variant ; p.Arg389Cys; MODERATE	nonsynonymous_codon ; R389C	Average:24.486; most accessible tissue: Minghui63 flag leaf, score: 38.911	benign	1.2	TOLERATED	0.06
vg0220796750	C -> DEL	LOC_Os02g34670.1	N	frameshift_variant	Average:24.486; most accessible tissue: Minghui63 flag leaf, score: 38.911	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220796750	NA	4.16E-06	mr1113	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
vg0220796750	NA	3.12E-19	mr1114	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
vg0220796750	4.14E-06	1.83E-08	mr1114	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
vg0220796750	NA	6.75E-06	mr1347	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

Showing 1 to 4 of 4 entries

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Search for Variation information by Variation ID:

Detailed information for vg0220796750:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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