RiceVarMap2

Detailed information for vg0514815080:

Variant ID: vg0514815080 (JBrowse)

Variation Type: SNP

Chromosome: chr05

Position: 14815080

Reference Allele: C

Alternative Allele: A

Primary Allele: C

Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TCATAAATATTCAACCTACTTGCGCTGTCACCGAAGCAACATCTAGCTTAATTGTTAATACTGCATGATGGCAAAGTTTTGTAGTTGTGGAGACATACTT[C/A]
AGGAATTAGGATGCTGCTTACTCAACTTCGAGATTGCATTGCGAAATTCTGCAGCACTTCTTTTTTTAAGGTATACTACCTGAGGTGACAGATACTTCCA

Reverse complement sequence

TGGAAGTATCTGTCACCTCAGGTAGTATACCTTAAAAAAAGAAGTGCTGCAGAATTTCGCAATGCAATCTCGAAGTTGAGTAAGCAGCATCCTAATTCCT[G/T]
AAGTATGTCTCCACAACTACAAAACTTTGCCATCATGCAGTATTAACAATTAAGCTAGATGTTGCTTCGGTGACAGCGCAAGTAGGTTGAATATTTATGA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.30%	9.10%	2.62%	0.00%	NA
All Indica	2759	81.00%	14.80%	4.24%	0.00%	NA
All Japonica	1512	98.70%	1.00%	0.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	71.40%	17.10%	11.43%	0.00%	NA
Indica II	465	74.40%	22.20%	3.44%	0.00%	NA
Indica III	913	92.00%	7.80%	0.22%	0.00%	NA
Indica Intermediate	786	79.40%	16.70%	3.94%	0.00%	NA
Temperate Japonica	767	98.30%	1.60%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	10.00%	3.33%	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
vg0514815080	C -> A	LOC_Os05g25480.1	upstream_gene_variant ; 1183.0bp to feature; MODIFIER	silent_mutation	Average:62.997; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N
vg0514815080	C -> A	LOC_Os05g25470-LOC_Os05g25480	intergenic_region ; MODIFIER	silent_mutation	Average:62.997; most accessible tissue: Minghui63 root, score: 78.833	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
vg0514815080	NA	8.38E-06	mr1578_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
vg0514815080	3.16E-06	NA	mr1647_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 2 of 2 entries

Previous1Next

Contact

Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China

Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/

Search for Variation information by Variation ID:

Detailed information for vg0514815080:

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