RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0316605932:

Variant ID: vg0316605932 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16605932
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.06, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTTTTGAGACTCTACATTCACAAGGATCTCAAACATGAATACATGTTAGAGACGAGCCCTCTCAACCTTTGGAAAGCTCTAAAAGAGCGTTATGATCA[G/T]
CAAAAGGAACTCATTTGGCCTGAGGCTAATTATGAGTGGGTTCATTTATGCCTACAGGACTTTAAAACTATGGCAGAATACAACCATGCTGTTCATAACA

Reverse complement sequence

TGTTATGAACAGCATGGTTGTATTCTGCCATAGTTTTAAAGTCCTGTAGGCATAAATGAACCCACTCATAATTAGCCTCAGGCCAAATGAGTTCCTTTTG[C/A]
TGATCATAACGCTCTTTTAGAGCTTTCCAAAGGTTGAGAGGGCTCGTCTCTAACATGTATTCATGTTTGAGATCCTTGTGAATGTAGAGTCTCAAAAGAA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.30%	14.20%	1.52%	0.00%	NA
All Indica	2759	89.10%	9.30%	1.59%	0.00%	NA
All Japonica	1512	83.50%	15.90%	0.60%	0.00%	NA
Aus	269	33.10%	59.90%	7.06%	0.00%	NA
Indica I	595	94.30%	5.00%	0.67%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	81.90%	14.60%	3.50%	0.00%	NA
Indica Intermediate	786	87.80%	11.20%	1.02%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	54.80%	43.50%	1.79%	0.00%	NA
Japonica Intermediate	241	92.10%	7.90%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	0.00%	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
vg0316605932	G -> T	LOC_Os03g29206.1	missense_variant ; p.Gln89His; MODERATE	nonsynonymous_codon ; Q89H	Average:33.837; most accessible tissue: Minghui63 flag leaf, score: 52.88	probably damaging	2.477	TOLERATED	0.18

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316605932	NA	3.06E-12	Grain_width	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0316605932	NA	4.05E-06	mr1073	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
vg0316605932	7.00E-07	2.52E-07	mr1113	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
vg0316605932	3.91E-06	2.92E-06	mr1119	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
vg0316605932	NA	7.53E-07	mr1345	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
vg0316605932	9.46E-07	1.09E-06	mr1917	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
vg0316605932	NA	8.84E-07	mr1188_2	Jap_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
vg0316605932	NA	4.40E-06	mr1638_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
vg0316605932	NA	5.73E-06	mr1736_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

Showing 1 to 9 of 9 entries

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Search for Variation information by Variation ID:

Detailed information for vg0316605932:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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