RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0134870908:

Variant ID: vg0134870908 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 34870908
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCATTATAAATATTGTAGTAAACACAGACGCTGCAATGGAAGCAGTGATTGTCCCTGCCAAAATACCAGCTAATGCGCCCCTCTTTAGACCTGATGAC[G/A]
CCACAGTTGGGAATTCTGCAAAATAAATTAAAAAGATATAAAAATAAGGGTAATTTTACCATCCTTAAAAAGGTAACTAGAGGTACCATATTTTTTAGTG

Reverse complement sequence

CACTAAAAAATATGGTACCTCTAGTTACCTTTTTAAGGATGGTAAAATTACCCTTATTTTTATATCTTTTTAATTTATTTTGCAGAATTCCCAACTGTGG[C/T]
GTCATCAGGTCTAAAGAGGGGCGCATTAGCTGGTATTTTGGCAGGGACAATCACTGCTTCCATTGCAGCGTCTGTGTTTACTACAATATTTATAATGAGA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.60%	44.30%	0.08%	0.00%	NA
All Indica	2759	26.10%	73.80%	0.14%	0.00%	NA
All Japonica	1512	98.10%	1.90%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	11.60%	88.40%	0.00%	0.00%	NA
Indica II	465	5.60%	94.00%	0.43%	0.00%	NA
Indica III	913	35.70%	64.30%	0.00%	0.00%	NA
Indica Intermediate	786	38.00%	61.70%	0.25%	0.00%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	2.40%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	70.00%	30.00%	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
vg0134870908	G -> A	LOC_Os01g60280.1	missense_variant ; p.Ala501Val; MODERATE	nonsynonymous_codon ; A501V	Average:61.582; most accessible tissue: Minghui63 flower, score: 80.659	benign	-0.302	TOLERATED	0.24

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
vg0134870908	NA	2.55E-25	mr1003	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
vg0134870908	NA	1.38E-06	mr1003	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
vg0134870908	NA	3.67E-06	mr1008	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
vg0134870908	NA	8.49E-25	mr1051	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
vg0134870908	NA	4.66E-06	mr1051	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
vg0134870908	NA	8.90E-21	mr1244	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
vg0134870908	NA	9.15E-09	mr1457	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
vg0134870908	NA	2.06E-06	mr1527	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
vg0134870908	NA	6.26E-07	mr1727	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
vg0134870908	NA	5.33E-06	mr1887	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 10 of 18 entries

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Search for Variation information by Variation ID:

Detailed information for vg0134870908:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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