RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0504314615:

Variant ID: vg0504314615 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 4314615
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.07, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GCACTCCCTCCTCATTTCTCCTCATCTCGACTCTGATTAAAAAAACAGACAGAGGGGGAGGAGAAGAGAAGAAGAGGCGAAGCCCTGCCGATTTGAGATC[C/T]
GATTTCAGGTAATATTTATAGATCCTATATGTGACTATTTAGTTAACTAGTGTGTATTTTTTAAAACTTTGTTTGAATAAATGCATTATACTCCCTCCAT

Reverse complement sequence

ATGGAGGGAGTATAATGCATTTATTCAAACAAAGTTTTAAAAAATACACACTAGTTAACTAAATAGTCACATATAGGATCTATAAATATTACCTGAAATC[G/A]
GATCTCAAATCGGCAGGGCTTCGCCTCTTCTTCTCTTCTCCTCCCCCTCTGTCTGTTTTTTTAATCAGAGTCGAGATGAGGAGAAATGAGGAGGGAGTGC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.50%	37.30%	0.28%	0.00%	NA
All Indica	2759	39.30%	60.30%	0.47%	0.00%	NA
All Japonica	1512	99.20%	0.80%	0.00%	0.00%	NA
Aus	269	78.10%	21.90%	0.00%	0.00%	NA
Indica I	595	16.10%	83.70%	0.17%	0.00%	NA
Indica II	465	56.30%	43.00%	0.65%	0.00%	NA
Indica III	913	40.50%	59.00%	0.44%	0.00%	NA
Indica Intermediate	786	45.20%	54.20%	0.64%	0.00%	NA
Temperate Japonica	767	98.70%	1.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	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
vg0504314615	C -> T	LOC_Os05g07950.1	upstream_gene_variant ; 4193.0bp to feature; MODIFIER	silent_mutation	Average:73.701; most accessible tissue: Minghui63 root, score: 90.94	N	N	N	N
vg0504314615	C -> T	LOC_Os05g07960.1	upstream_gene_variant ; 257.0bp to feature; MODIFIER	silent_mutation	Average:73.701; most accessible tissue: Minghui63 root, score: 90.94	N	N	N	N
vg0504314615	C -> T	LOC_Os05g07970.1	upstream_gene_variant ; 662.0bp to feature; MODIFIER	silent_mutation	Average:73.701; most accessible tissue: Minghui63 root, score: 90.94	N	N	N	N
vg0504314615	C -> T	LOC_Os05g07980.1	downstream_gene_variant ; 2882.0bp to feature; MODIFIER	silent_mutation	Average:73.701; most accessible tissue: Minghui63 root, score: 90.94	N	N	N	N
vg0504314615	C -> T	LOC_Os05g07960-LOC_Os05g07970	intergenic_region ; MODIFIER	silent_mutation	Average:73.701; most accessible tissue: Minghui63 root, score: 90.94	N	N	N	N

Showing 1 to 5 of 5 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0504314615	2.20E-06	NA	mr1117	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 1 of 1 entries

Previous1Next

Search for Variation information by Variation ID:

Detailed information for vg0504314615:

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