RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0623386254:

Variant ID: vg0623386254 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 23386254
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TCATTCTTTCCTAGAGAAACCCCTAATTTAGAAAAATTTGCAGCAAGAGTCTTATCTGGAATTGAAGCAACAGAATTTGTGGTATTAAACTTGTTACCTG[T/C]
TAGCGTCTCGAGGTTATGAACCTTTTTAAGCAGCTCTGCCCGGTTTGCCACCGGCGCATCTGCATTTGCCATCGCCTTCTGTCTTTCACTTTGCCTAGTT

Reverse complement sequence

AACTAGGCAAAGTGAAAGACAGAAGGCGATGGCAAATGCAGATGCGCCGGTGGCAAACCGGGCAGAGCTGCTTAAAAAGGTTCATAACCTCGAGACGCTA[A/G]
CAGGTAACAAGTTTAATACCACAAATTCTGTTGCTTCAATTCCAGATAAGACTCTTGCTGCAAATTTTTCTAAATTAGGGGTTTCTCTAGGAAAGAATGA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.20%	6.50%	5.63%	49.75%	NA
All Indica	2759	45.90%	11.00%	6.34%	36.72%	NA
All Japonica	1512	21.10%	0.00%	0.99%	77.91%	NA
Aus	269	58.70%	0.00%	25.28%	15.99%	NA
Indica I	595	49.60%	9.90%	9.75%	30.76%	NA
Indica II	465	32.90%	11.40%	2.80%	52.90%	NA
Indica III	913	52.70%	11.80%	5.81%	29.68%	NA
Indica Intermediate	786	43.00%	10.70%	6.49%	39.82%	NA
Temperate Japonica	767	34.20%	0.00%	1.17%	64.67%	NA
Tropical Japonica	504	6.20%	0.00%	0.99%	92.86%	NA
Japonica Intermediate	241	10.80%	0.00%	0.41%	88.80%	NA
VI/Aromatic	96	27.10%	0.00%	4.17%	68.75%	NA
Intermediate	90	36.70%	2.20%	4.44%	56.67%	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
vg0623386254	T -> C	LOC_Os06g39400.1	missense_variant ; p.Thr684Ala; MODERATE	nonsynonymous_codon ; T684A	Average:58.043; most accessible tissue: Minghui63 root, score: 71.702	unknown	unknown	TOLERATED	0.85
vg0623386254	T -> DEL	LOC_Os06g39400.1	N	frameshift_variant	Average:58.043; most accessible tissue: Minghui63 root, score: 71.702	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0623386254	NA	3.09E-06	mr1547	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
vg0623386254	1.08E-09	6.69E-12	mr1709	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
vg0623386254	1.14E-08	3.20E-10	mr1709	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
vg0623386254	NA	9.76E-07	mr1547_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
vg0623386254	NA	3.27E-08	mr1547_2	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
vg0623386254	5.43E-14	9.24E-12	mr1709_2	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
vg0623386254	3.60E-10	1.54E-10	mr1709_2	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

Showing 1 to 7 of 7 entries

Previous1Next

Search for Variation information by Variation ID:

Detailed information for vg0623386254:

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