RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0728265516:

Variant ID: vg0728265516 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 28265516
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.03, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TCCTGTGCAAATCAATTTAACAACTATGTATTGATGTCCTCATACTCTCTGTTATTTTAGGTCATTCCAACTATGGCGAGAAAGTGTCTGTTGATCAGGA[A/G]
GGAGCAAACAATTCTACTCTTTCACCATATATGGGAGGTCCTGCTTTGATGGATGATTCTCCTGCATCTAAAATGGCTTTGGAGCATAGCATTACGACAT

Reverse complement sequence

ATGTCGTAATGCTATGCTCCAAAGCCATTTTAGATGCAGGAGAATCATCCATCAAAGCAGGACCTCCCATATATGGTGAAAGAGTAGAATTGTTTGCTCC[T/C]
TCCTGATCAACAGACACTTTCTCGCCATAGTTGGAATGACCTAAAATAACAGAGAGTATGAGGACATCAATACATAGTTGTTAAATTGATTTGCACAGGA

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	51.30%	48.10%	0.63%	0.00%	NA
All Indica	2759	67.30%	31.90%	0.72%	0.00%	NA
All Japonica	1512	29.00%	70.60%	0.46%	0.00%	NA
Aus	269	5.60%	94.10%	0.37%	0.00%	NA
Indica I	595	41.80%	55.80%	2.35%	0.00%	NA
Indica II	465	88.60%	10.80%	0.65%	0.00%	NA
Indica III	913	72.10%	27.80%	0.11%	0.00%	NA
Indica Intermediate	786	68.60%	31.20%	0.25%	0.00%	NA
Temperate Japonica	767	1.40%	97.90%	0.65%	0.00%	NA
Tropical Japonica	504	73.80%	26.00%	0.20%	0.00%	NA
Japonica Intermediate	241	22.80%	76.80%	0.41%	0.00%	NA
VI/Aromatic	96	69.80%	29.20%	1.04%	0.00%	NA
Intermediate	90	51.10%	47.80%	1.11%	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
vg0728265516	A -> G	LOC_Os07g47284.1	intron_variant ; MODIFIER	silent_mutation	Average:48.06; most accessible tissue: Callus, score: 69.457	N	N	N	N

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0728265516	NA	2.83E-12	mr1241	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
vg0728265516	NA	1.20E-06	mr1277	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
vg0728265516	NA	1.07E-11	mr1410	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
vg0728265516	NA	1.69E-07	mr1551	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
vg0728265516	NA	3.33E-06	mr1740	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
vg0728265516	2.39E-06	NA	mr1099_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
vg0728265516	2.05E-07	6.71E-14	mr1304_2	Jap_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
vg0728265516	NA	3.42E-10	mr1308_2	Jap_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
vg0728265516	NA	2.04E-09	mr1327_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
vg0728265516	NA	2.38E-09	mr1347_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 10 of 43 entries

Previous1 2 3 4 5Next

Search for Variation information by Variation ID:

Detailed information for vg0728265516:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

RiceVarMap v2.0

Tools

Blast

Design Primer by Variation ID

Design Primer by Region

Haplotype Network Analysis

Varitation Coordinate Convert

Contact